title: Naturally restored secondary forests_rep4

value: Hunan Province Hengyang County

value: Liquidambar formosana Hance, Pinus massoniana Lamb., Castanopsis sclerophylla (Lindl.) Schott., and Quercus fabri Hance


title: Muscle of wild type mouse - rep 5

status: Public on Nov 04 2019

type: RNA

city: Sevilla

first: Daniel Jose

last: Moreno Fernandez-Ayala

address: Carretera de Utrera, Km. 1

country: Spain

institute: Universidad Pablo de Olavide

description:
replicate 5
M-WT_5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Mouse gastronomius muscle

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed by RNA electrophoresis and with Agilent Bioanalyser.

tag: genotype/variation

value: wild type

tag: strain

tag: age

value: 3 year old

tag: tissue

value: muscle


title: PMD000018_Cap26

type: SRA

city: Kansas City

first: Elin

last: Grundberg

state: Missouri

address: 2401 Gillham Road

country: USA

institute: CHILDREN'S MERCY HOSP (KANSAS CITY, MO)

library_source: transcriptomic

data_processing:
Primary Analysis of demultiplexing, barcode correcting, alignment and generation of gene expression matrix was done using cellranger v.2.1.0 from 10X Genomics using GRCh38 as reference. The demuxlet software (Kang et al, Nature Biotechnology 2017) was used for further genetic multiplexing and removal of multiplets.
Seurat v. 3.0.1 was then used for downstream analysis of filtering, Normalization, clustering and dimensionality reduction.
We removed cells with low gene count (<200), high mitochondrial gene expression (> 40%), high Gene count (>6,000) and high UMI count (>50,000).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab delimited file containing normalized, log transformed expression matrix

molecule: polyA RNA

organism: Homo sapiens

source_name: SVF from Adipose Tissue

extract_protocol:
Adipose tissue was digested with collagenase according to a modification of the Robdell method (Tchernof et al., 2006). Briefly, adipose tissue samples were digested with collagenase type 1 in Krebs-Ringer-Henseleit (KRH) buffer for 45 minutes at 37°C. Cell suspensions containing mature adipocytes and the stromal-vascular fraction (SVF) were then filtered with a 150um nylon mesh and washed 3 times with Hank’s Balanced Salt Solution (HBSS) supplemented with 200um adenosine and 2% FBS and centrifuged at 200 rcf for 8 minutes. The nature of the buoyancy adipocytes allows them to float to the surface during the centrifugation step. Mature adipocytes were discarded and the remaining solution containing the SVF was centrifuged 300 rcf for 6 minutes. The pellet was washed with HBSS+200um adenosine+2%FBS followed by centrifugation. The pellet was treated with ACK lysis buffer at RT for 5 minutes, followed by another centrifugation step. The ACK lysis buffer was removed from the pellet and the cells were washed once more with HBSS+200uM adenosine+2%FBS and centrifuged one final time. Cells were counted to determine the total number of cells in suspension and viability. Cells were then cryopreserved using freezing medium (Gibco™ Recovery™ Cell Culture Freezing Medium, 10% DMSO). The medium was added to the pellet and was frozen with a temperature gradient (-1 °C/ minutes) and stored in liquid nitrogen until analysis.
Cells from the SVF were thawed and serially diluted in DMEM/F12 supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin in 15ml conical tube to a volume of 14ml. They were centrifuged at 300 rcf for 10 minutes and the supernatant was removed and discarded. The pelleted cells were suspended in an adequate amount of DMEM/F12 supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin and transferred to a 1.5ml microfuge tube for counting. 10 µl of the suspension was used for a cell count and viability assay on a Countess II Automated Cell Counter (Invitrogen) to determine the volume of suspension to be used in the 10x Chromium Single Cell Library protocol. The desired number of viable cells to be loaded onto two wells of a Chromium Single Cell A Chip (10x Genomics) was 8000 cells for a total of two captures with 4000 cells/capture. After cell capture, the remaining cells were centrifuged at 300 rcf for 10 minutes and cryopreserved using freezing medium (Recovery Cell Culture Freezing Medium, Thermo Fisher Scientific). The cells were suspended in freezing medium and frozen with a temperature gradient of -1⁰C per minute and stored in liquid nitrogen. Cell capture, cDNA amplification, and library preparation were performed using the Chromium Single Cell 3' Library & Gel Bead Kit v2 (10x Genomics), according to the manufacturer’s protocol. The final two libraries were analyzed using a TapeStation to determine library size and a Qubit Broad Range dsDNA assay to determine library concentration and sequenced on Illumina NovaSeq6000 instrument.

value: Visceral adipose tissue


title: Muscle of ADCK2(+/-) mutant mouse - rep 2

description:
replicate 2
M-ADCK2_2

value: ADCK2(+/-) mutant


title: PMD000018_Cap25


title: TCR_HC15

city: Stanford

first: Olivia

last: Leventhal

state: California (CA)

address: 1201 Welch Road, rm p220

department: Neurology

institute: Stanford University

data_processing:
Library strategy: single cell TCR-seq
Real-Time Analysis (RTA) software called RTA2 used for basecalling.
Base call files were demultiplexed using cellranger mkfastq version 3.0.2
TCR-seq reads were mapped alligned to the GRCh38 2.0.0 vdj genome assembly available from 10X Genomics using cellranger count version 3.0.2
T cell receptor sequences were generated using cellranger vdj version 3.0.2
Genome_build: GRCh38 vdj 2.0.0
Supplementary_files_format_and_content: two files for each sample; one file that indicates clonotypes and one file that has the sequence for each cell barcode

source_name: cerebrospinal fluid derived cells

extract_protocol:
CSF cells were Live cell sorted using an LSRFortessa (BD Biosciences). RNA was extracted according to the 10x v2 5' Expression library kit.
Libraries were prepared  according to the 10x v2 5' V(D)J Kit.

value: cerebrospinal fluid

tag: cell type

value: T cells

tag: diagnosis

value: HC


title: CSF_MCI7

data_processing:
Real-Time Analysis (RTA) software called RTA2 used for basecalling.
Base call files were demultiplexed using cellranger mkfastq version 3.0.2
RNA-seq reads were mapped alligned to the GRCh38 3.0.0 genome assembly available from 10X Genomics using cellranger count version 3.0.2
Gene expression matrices were generated using cellranger count version 3.0.2
Gene expression matrices for each sample were loaded into the R package 'Seurat' v3.0 and all samples  were merged into one Seurat object
Genome_build: GRCh38 3.0.0
Supplementary_files_format_and_content: tar archive for each sample containing expression matrix, cellbarcodes, and genes

extract_protocol:
CSF cells were Live cell sorted using an LSRFortessa (BD Biosciences). RNA was extracted according to the 10x v2 5' Expression library kit.
Libraries were prepared  according to the 10x v2 5' Expression library kit.

value: immune cells

value: MCI


title: Naturally restored secondary forests_rep3

type: genomic

city: Beijing

first: Yun

last: Wang

address: Shuangqing Road 18th, Haidian District

country: China

institute: Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences

hyb_protocol: The labeled DNA was suspended in 120 µl hybridization solution (50% formamide, 3 × SSC, 10 µg of unlabeled herring sperm DNA (Promega, Madison, WI), and 0.1% SDS. The mix was kept at 95°C for 5 min and kept at 50°C until deposited onto a microarray. Hybridizations were performed with a TECAN Hybridization Station HS4800 Pro (TECAN, US) (Xue et al. 2007) (K. Xue, M.M. Yuan, J.P. Xie, D. Li, Y. Qin, L. E. Hale, L. Wu, Y. Deng, Z. He, J. D. Van Nostrand, Y. Luo, J. M. Tiedje, J. Zhou. Annual removal of aboveground plant biomass alters soil microbial responses to warming. mBio 7, 1-12 (2016)).

scan_protocol: The hybridized GeoChip 3.0 was scanned with a ScanArray 5000 (Perkin-Elmer, Wellesley, MA, USA) at 95% laser energy and 85% photomultiplier tube gain, and digitally analyzed using Imagene software (6.0 premium version, Biodiscovery, El Segundo, CA, USA)

data_processing: The data were processed as follows: (i) Probes flagged as 1 or 3 by ImaGene and probes with signal to noise ratio < 2.0 were removed; (ii) Data were normalized firstly within a slide，then among samples，and finally devided by the mean of the signal intensities of all probes; (iii) Probes appeared less than 3 times for each reforestation approach were deleted; (iv) Samples with probe numbers outside of mean ± (2 × standard error) were considered outliers (ARMP1, NRSF2, and NRSF7) and removed. In total, 14, 14, and 11 microarray replicates were obtained for ARSP, ARMP, and NRSF, respectively.

molecule: genomic DNA

organism:
Bacteria
Archaea
Fungi
Viruses

source_name: Naturally restored secondary forests

label_protocol: The DNA was labeled by Cy5 as described (Xue et al. 2007). Firstly, the DNA was mixed with 20 μL random primers, denatured at 99.9 °C for 5 min, and chilled on ice. Secondly, the labeling master mix (2.5 μL dNTP (5 mM dAGC-TP, 2.5 mM dTTP), 1 μL Cy-5 dUTP (Amersham, Piscataway, NJ), 80 U of the large Klenow fragment (Invitrogen, Carlsbad, CA), and 2.5 μL water) were added, incubated at 37°C for 3 h, and then heated at 95 °C for 3 min. Thirdly, the labeled DNA was purified with the QIA quick purification kit (Qiagen, Valencia, CA), measured on a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE), and then dried in a SpeedVac (ThermoSavant, Milford, MA) at 45 °C for 45 min (Xue et al. 2007). (K. Xue, M.M. Yuan, J.P. Xie, D. Li, Y. Qin, L. E. Hale, L. Wu, Y. Deng, Z. He, J. D. Van Nostrand, Y. Luo, J. M. Tiedje, J. Zhou. Annual removal of aboveground plant biomass alters soil microbial responses to warming. mBio 7, 1-12 (2016)).

growth_protocol: Soil samples were collected from the top 10 cm in October 2008 and August, September 2009. Each sample was composition of fifteen soil cores (3.5 cm diameter). All samples were sieved through 2 mm sieves, and stored at -80 °C.

extract_protocol: Soil DNA was extracted by phenol/chloroform method with Al2(SO4)3 pretreatment (Peršoh et al. 2008). Firstly, 0.5 g soil was washed with an excess Al2(SO4)3 (0.2 M) which was subsequently removed with a 4 M NaOH solution. Secondly, DNA and protein were extracted from soil with Tris-HCl buffer (0.4 M LiCl, 100 mM Tris–HCl, 120 mM EDTA, pH 8) and 0.5 g glass beads by glass beading. Thirdly, DNA and protein were separated with phenol:chloroform:alcohol (25:24:1) and chloroform:isoamyl alcohol (24:1), and the supernatant was washed with chloroform overnight. Fourthly, DNA was precipitated twicely with 70% cold ethanol at 13000 rpm for 60 min and 15 min, respectively (Peršoh et al. 2008). (D. Peršoh, S. Theuerl, F. Buscot, G. Rambold, Towards a universally adaptable method for quantitative extraction of high-purity nucleic acids from soil. J. Microbiol. Meth. 75, 19-24 (2008)).

treatment_protocol: The forests have been restored for about tweenty years. The restored forests were naturally restored secondary forests (NRSF), artificial reforestation with native Masson pine (Pinus massoniana Lamb.) (ARMP), and introduced slash pine (Pinus elliottii Engelm.) plantations (ARSP). For each forest restoration method, 15 plots (500 m × 500 m) were studied. Fifteen soil cores were collected from each plot, and then combined to create a composite sample.

tag: site

tag: dominant tree species


title: Naturally restored secondary forests_rep7

value: Jiangxi Province Anfu County

value: Cinnamomum camphora L. and Cunninghamia lanceolata (Lamb.) Hook.


title: TCR_MCI6


title: Naturally restored secondary forests_rep2


title: Artificial restored Masson pine plantations_rep13

source_name: Artificially restored Masson pine plantations

value: Guangxi Province Guilin City

value: Pinus massoniana Lamb.


title: Naturally restored secondary forests_rep1


title: Naturally restored secondary forests_rep5


title: TCR_MCI5


title: CSF_AD9

value: AD


title: Muscle of wild type mouse - rep 4

description:
replicate 4
M-WT_4


title: Artificial restored Masson pine plantations_rep14


title: TCR_PD5

value: PD


title: CSF_MCI6


title: TCR_HC14


title: WT_Unstim_rep2

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

description: NMC035_1604969_ClariomSmouse.rma-gene-full-Signal

hyb_protocol: Six micrograms of biotinylated cDNA was fragmented and then hybridized for 16 hr at 45C on an Affymetrix GeneChip. Following hybridization, GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the AffymetrixGeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console software v1.1

source_name: WT_Unstim_CD4+CD25+ Tregs

label_protocol: Total RNA (1 - 20 ng) were converted into biotinylated cDNA using the NuGEN WTA Pico v2 protocol and the NuGEN Encore Biotin module

growth_protocol: Lymphocytes were enriched using CD4 MicroBeads (Miltenyi Biotec) according to manufacturer’s instructions, and then stained and sorted for CD25+CD4+ Tregs.

extract_protocol: Total RNA samples were prepared according to the prototol of Rneasy Micro kit from Qiagen,

treatment_protocol: Sorted cells were lysed with lysis buffer from Rneasy Micro kit from Qiagen.

tag: strain background

value: WT

value: CD4+CD25+ Tregs

tag: treatment

value: unstimulated


title: TCR_HC13


title: CSF_MCI5


title: Muscle of ADCK2(+/-) mutant mouse - rep 4

description:
replicate 4
M-ADCK2_4

value: 3 year old

value: muscle


title: TCR_MCI4


title: Artificial restored Masson pine plantations_rep12


title: Muscle of wild type mouse - rep 1

description:
replicate 1
M-WT_1

value: wild type


title: TCR_PD4

value: cerebrospinal fluid


title: Artificial restored Masson pine plantations_rep11


title: Liver of ADCK2(+/-) mutant mouse - rep 5

description:
replicate 5
L-ADCK2_5

source_name: Mouse liver

value: ADCK2(+/-) mutant

value: liver


title: Muscle of wild type mouse - rep 3

description:
replicate 3
M-WT_3


title: TCR_AD8

value: T cells


title: CSF_MCI4

value: immune cells

value: MCI


title: Artificial restored Masson pine plantations_rep10


title: Muscle of ADCK2(+/-) mutant mouse - rep 3

description:
replicate 3
M-ADCK2_3


title: CSF_AD8


title: TCR_HC12

value: HC


title: Artificial restored Masson pine plantations_rep9

value: Jiangxi Province Anfu County


title: Liver of ADCK2(+/-) mutant mouse - rep 3

description:
replicate 3
L-ADCK2_3


title: head RsCDX2::Sox2CreERT2, 3

city: Nantes

first: Victor

last: GOURAIN

address: 30 Bd Jean Monnet

country: France

institute: Centre de recherche en transplantation et immunologie

data_processing:
Read quality assessment (FASTX-toolkit)
Read alignment (STAR v2.5)
Read counting at gene level (HTSeq v0.6.1)
Expression normalization and differential gene expression analysis (DESeq2 v1.10.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: HTSeq raw count

source_name: head Cdx2 expression embryo 3

extract_protocol:
total RNA extracted from embryonic mouse head in TriReagent (Euromedex)
Illumina TruSeq stranded mRNA

treatment_protocol: single intraperitonal injection of 2 mg Tamoxifen to the mother at day 6.5 post coitum

tag: genotype

value: head down to the rhombomere 2 and pharyngeal arch 1


title: head RsCDX2::Sox2CreERT2, 2

source_name: head Cdx2 expression embryo 2

value: single intraperitonal injection of 2 mg Tamoxifen to the mother at day 6.5 post coitum


title: TCR_AD7

value: AD


title: Liver of ADCK2(+/-) mutant mouse - rep 2

description:
replicate 2
L-ADCK2_2


title: Artificial restored Masson pine plantations_rep6

value: Pinus massoniana Lamb.


title: Artificial restored Masson pine plantations_rep8


title: Liver of ADCK2(+/-) mutant mouse - rep 4

description:
replicate 4
L-ADCK2_4


title: CSF_AD7


title: Liver of ADCK2(+/-) mutant mouse - rep 1

description:
replicate 1
L-ADCK2_1


title: Artificial restored Masson pine plantations_rep7


title: Artificial restored Masson pine plantations_rep5


title: head RsCDX2::Sox2CreERT2, 1

source_name: head Cdx2 expression embryo 1


title: TCR_MCI3


title: Artificial restored Masson pine plantations_rep4

value: Hunan Province Hengyang County


title: CSF_MCI3


title: head Sox2CreERT2, 2

source_name: head control 3

value: single intrperitonal injection of 2 mg Tamoxifen to the mother at day 6.5 post coitum


title: TCR_HC11


title: TCR_PD3

value: PD


title: TCR_HC10


title: Liver of wild type mouse - rep 5

description:
replicate 5
L-WT_5

value: 3 year old


title: Liver of wild type mouse - rep 1

description:
replicate 1
L-WT_1

value: wild type


title: Artificial restored Masson pine plantations_rep3


title: Liver of wild type mouse - rep 4

description:
replicate 4
L-WT_4


title: Liver of wild type mouse - rep 2

description:
replicate 2
L-WT_2


title: head Sox2CreERT2, 1

source_name: head control 1


title: TCR_AD6

value: cerebrospinal fluid


title: CSF_AD6


title: Artificial restored Masson pine plantations_rep1


title: OGT-deficient liver tissue [OGT_KO_4]

city: New Haven

first: Xiaoyong

last: Yang

state: CT

address: 375 Congress Ave

department: Comparative Medicine

institute: Yale University

data_processing:
Sequencing reads were aligned against the mouse mm10 reference genome using the TopHat2 software version 2.1.0 with the default parameters.
Mapped reads were assigned to gene features and quantified using the HTSeq software version 0.9.1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include HTSeq raw abundance values for each sample.

source_name: Liver tissue

extract_protocol: Total RNA was extracted from liver tissue with TRIzol reagent according to the manufacturer's protocol.

tag: strain/background

value: OGT-deficient

value: Liver


title: Artificial restored slash pine plantations_rep14

source_name: Artificially restored slash pine plantations

value: Guangxi Province Guilin City

value: Pinus elliottii Engelm.


title: OGT-deficient liver tissue [OGT_KO_2]


title: Liver of wild type mouse - rep 3

description:
replicate 3
L-WT_3

value: liver


title: HC17

source_name: peripheral blood mononuclear cells

extract_protocol:
TEMRA cells were Live cell sorting using an LSRFortessa (BD Biosciences). See Extended Data Figure 8 for gating strategy. RNA was extracted according to the 10x v2 5' Expression library kit.
Libraries were prepared  according to the 10x v2 5' Expression library kit.

value: blood

value: CD8+ TEMRA cells

value: Healthy


title: Artificial restored Masson pine plantations_rep2


title: Artificial restored slash pine plantations_rep10


title: Artificial restored slash pine plantations_rep12


title: Artificial restored slash pine plantations_rep11


title: HC13


title: Wildtype liver tissue [OGT_WT_5]

value: Wildtype


title: AD9

value: AD


title: Wildtype liver tissue [OGT_WT_2]


title: OGT-deficient liver tissue [OGT_KO_3]


title: Artificial restored slash pine plantations_rep13


title: AX4 Lp_6hpi-B

city: Uppsala

first: Erik

last: Holmqvist

state: Uppland

address: Husargatan 3, Box 596, Uppsala University, Dept. of Cell and Molecular Biology

country: Sweden

institute: Uppsala University

data_processing:
Alignment of poly(A) RNA-seq reads using TopHat v.2.0.13
Read counts performed with featureCounts v 1.6.2 using gene annotations generated Aug. 24th 2018 from www.dictybase.org
Genome_build: D. discoideum (05-13-2009)
Supplementary_files_format_and_content: tab-delimited raw read count tables

organism: Dictyostelium discoideum AX4

source_name: Cell culture

growth_protocol: For M. marinum infection samples: Dictyostelium discoideum AX2 cells were cultured axenically at 22°C in 10 ml HL5-C medium without glucose pH 6.4 (Formedium) supplemented after autoclavation with 1% glucose and 100 U/ml Penicillin-Streptomycin (Gibco by Life Technologies). The cells were grown adherent to plastic in BD Falcon tissue culture dishes (100 × 20 mm). Antibiotics were excluded from the growth medium the day before and during infection experiments.  Mycobacterium marinum M strain carrying the msp12::gfp plasmid, constitutively expressing GFP, was used in the infection experiments (Hagedorn and Soldati, 2007).  Bacteria were grown on 7H10 agar (Difco Middlebrook, BD) containing 10% OADC supplement (oleic acid, albumin, dextrose, catalase; Difco) and 0.5% glycerol, or cultivated in 7H9 broth (Difco Middlebrook, BD) supplemented with OADC, 0.2% glycerol and 0.05% Tween80 (Sigma Aldrich) at 32°C shaking culture with glass beads to decrease bacterial clumping. Both 7H10 agar and 7H9 broth were supplemented with 50 µg/ml kanamycin to maintain the msp12::gfp plasmid. Growth of D. discoideum AX4 and L. pneumophila Lp01 is described in Li et al., 2009 (DOI:10.1016/j.chom.2009.08.005).

extract_protocol:
For M. marinum infection samples, total RNA was isolated by the Ambion PureLink™ RNA Mini kit in combination with TRIzol (Invitrogen), followed by on column DNAse treatment according to the manufacturer’s instructions (Ambion, Invitrogen). For L. pneumophila infection samples RNA samples were prepared by TRIzol extraction.
For M. marinum infection samples, poly(A)-enriched libraries were created using TruSeq RNA Library Prep Kit (Illumina). For L. pneumophila infected samples, libraries were prepared using TruSeq stranded mRNA library preparation kit with polyA selection (Illumina).

treatment_protocol: Experimental procedure for M. marinum infection samples: the day before infection, BD Falcon tissue culture dishes (100 × 20 mm) were seeded with D. discoideum AX2 cells and grown without antibiotics overnight to 2x10^7 cells per plate. M. marinum were collected and resuspended in HL5-C, bacterial clumps were disrupted by passing through a blunt end 26-gauge needle whereafter bacteria was added to the amoeba at MOI ~200. Non-infected samples were prepared simultaneously and treated identically except for the addition of bacteria. The infection was initiated by centrifugation at 500xg twice for 7 minutes or three times for 5 minutes followed by incubation at 25°C for 50 min post infection  to allow for uptake of bacteria. Subsequently, extracellular M. marinum cells were removed by five washes with HL5-C  after which the cells were incubated at 25°C. The cells were collected in HL5-C approximately 2 hours after initiation of infection and a subsample was added to the same volume of Soerensen buffer (2g KH2PO4 and 0.27g Na2HPO4 in 1L water, pH 6) + 5mM Sodium azide (Sigma). Samples were analyzed in a BD Accuri C6 flow cytometer in Soerensen buffer + 20 mM sorbitol. Experimental procedure for L. pneumophila infection samples is described in Li et al., 2009 (DOI:10.1016/j.chom.2009.08.005).

tag: infection

value: Legionella pneumophila infected 6 hpi


title: Wildtype liver tissue [OGT_WT_4]


title: Artificial restored slash pine plantations_rep7

value: Jiangxi Province Anfu County


title: Wildtype liver tissue [OGT_WT_1]


title: Wildtype liver tissue [OGT_WT_3]


title: Artificial restored slash pine plantations_rep6


title: HC16


title: AX4 Lp_1hpi-B

value: Legionella pneumophila infected 1 hpi


title: Artificial restored slash pine plantations_rep5


title: OGT-deficient liver tissue [OGT_KO_1]


title: AX2 Mm_2.5hpi-B

organism: Dictyostelium discoideum AX2

value: Mycobacterium marinum infected appr. 2.5 hpi


title: head WT

source_name: head control 2

value: WT

value: single intraperitonal injection of 2 mg Tamoxifen to the mother at day 6.5 post coitum

value: head down to the rhombomere 2 and pharyngeal arch 1


title: Artificial restored slash pine plantations_rep9


title: AX2 Mm_2.5hpi-A


title: Artificial restored slash pine plantations_rep4

value: Hunan Province Hengyang County


title: Artificial restored slash pine plantations_rep8


title: AX4 Non-inf-B

value: non-infected ctrl


title: AX4 Lp_1hpi-A


title: AX4 Lp_6hpi-A


title: AX2 Non-inf-B


title: Artificial restored slash pine plantations_rep3


title: AX2 Non-inf-A


title: TCR_PD6

value: cerebrospinal fluid

value: T cells

value: PD


title: AX4 Non-inf-A


title: SK-N-FI Input histone-ChIP-Seq

status: Public on Nov 03 2019

city: Philadelphia

first: Jo Lynne

last: Rokita

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

library_source: genomic

data_processing:
FASTQ sequences were adapter and quality trimmed using TrimGalore.
Phred scores were calculated per sample and used during hg19 alignment with bwa samse.
Picard tools v.2.17.9-SNAPSHOT was used to remove duplicate reads.
Fragment sizes were estimated using MaSC and these values were used as input into MACS2 for broad peak calling.
Peaks were called significant using a q-value cut off of 0.05 and results were returned in units of signal per million reads.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: neuroblastoma-derived cell line

growth_protocol: Cells were grown in 150 mm cell culture plates with appropriate media until ~70-80%.

extract_protocol:
For ChIP-Seq, cells were crosslinked, flash frozen, and sent to Active Motif. According to Active Motif protocol, cells were lysed, sonicated, and then DNA-protein complexes were isolated with antibodies. Samples were reverse-crosslinked and DNA was purified. For ATAC-Seq, whole cells were frozen and sent to Active Motif for thawing and transposition.
Illumina libraries were prepared by Active Motif using standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After 15 cycles of PCR amplification, the resulting DNA libraries were quantified and sequenced by Jefferson Cancer Genomics Laboratory at the Kimmel Cancer Center using the NexSeq 500.

tag: growth media

value: RPMI 1640, 10% FBS, 1% Penicillin/Streptomycin, 2mM L-Glutamine

tag: cell line

value: SK-N-FI

tag: chip antibody


title: SK-N-FI H3K27me3 histone-ChIP-Seq


title: SK-N-FI H3K4me3 histone-ChIP-Seq

value: H3K4me3 (Active Motif, #39159)


title: SK-N-FI H3K27Ac histone-ChIP-Seq

value: H3K27Ac (Active Motif, #39133)


title: Artificial restored slash pine plantations_rep1

value: Pinus elliottii Engelm.


title: SK-N-BE(2)-C Input histone-ChIP-Seq


title: Artificial restored slash pine plantations_rep2


title: SK-N-BE(2)-C H3K4me3 histone-ChIP-Seq


title: SK-N-BE(2)-C H3K27Ac histone-ChIP-Seq


title: SK-N-BE(2)-C H3K27me3 histone-ChIP-Seq


title: QMY_TREATED

city: Debrecen

first: Krisztina

last: Szabó

address: Egyetem tér

department: Medical Chemistry

country: Hungary

institute: University of Debrecen

hyb_protocol: The slide was hybridized at 65°C and 10 rpm for 17 h in an Agilent hybridization oven.

scan_protocol: The slide was scanned with Agilent DNA Microarray Scanner (FE SW 11.1) using one color scan setting for 1x44k array slides (Extended Dynamic Range, Scan Area 61x21.6 mm, Scan resolution 5 m, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%)

data_processing: Prenormalised microarray data were obtained with Agilent's Feature Extraction software (version 12.0.3.1) using default one-color high density protocol. Prenormalised data were background corrected using the normexp+offset method  followed by quantile normalization between arrays.

organism: Candida albicans

source_name: fungal cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared according to Agilent's One-Color Labeling protocol (version 6.7)

growth_protocol: Strains were maintained on YPDA (1% yeast extract, 2% mycological peptone, 2% glucose, 2% agar, pH 5.6). Pre-cultures were grown in YPD medium at 37°C without shaking and 18 h cultures were used to inoculate main cultures. Main cultures (20 mL YPD; starting OD640 = 0.1) were incubated at 37°C with 140 rpm shaking.

extract_protocol: Total RNA was isolated using TRISOL reagent (Invitrogen, Austria) reagent (Chomczynski BioTechniques. 1993; 15:536–7.) from cell free extracts prepared with glass beads. RNA concentrations were determined using NanoDrop (Thermo Scientific) and their quality were checked by Bioanalyser (Agilent) using Eukaryotic Total RNA Nano Kit according to the manufacturer's protocol.

treatment_protocol: Main cultures were treated at 4 h with tert-butyl-hydroperoxide (final concentration: 0.4 mM) and were further incubated for 1 h. Fungal cells were collected by centrifugation (10 min, RCF=7750g, 4°C) at 5 h. The cells were washed two times with phosphate-buffered saline and stored at -70°C until use.

tag: background strain

value: wild type


title: SK-N-AS H3K4me1 histone-ChIP-Seq

value: SK-N-AS

value: H3K4me1 (Active Motif, #39297)


title: SK-N-BE(2)-C H3K4me1 histone-ChIP-Seq


title: SK-N-AS H3K27Ac histone-ChIP-Seq


title: SK-N-FI H3K4me1 histone-ChIP-Seq


title: SK-N-AS H3K27me3 histone-ChIP-Seq


title: KO_TREATED

value: cappz1 mutant


title: NGP Input histone-ChIP-Seq

value: NGP


title: Muscle of wild type mouse - rep 2

description:
replicate 2
M-WT_2

source_name: Mouse gastronomius muscle

tag: genotype/variation

value: 3 year old

value: muscle


title: NBL-S Input histone-ChIP-Seq

value: NBL-S


title: NGP H3K27Ac histone-ChIP-Seq


title: SK-N-AS H3K4me3 histone-ChIP-Seq


title: NGP H3K27me3 histone-ChIP-Seq


title: NGP H3K4me1 histone-ChIP-Seq


title: QMY_CTRL


title: SK-N-AS Input histone-ChIP-Seq


title: NBL-S H3K4me3 histone-ChIP-Seq


title: NB-69 Input histone-ChIP-Seq


title: NBL-S H3K27me3 histone-ChIP-Seq


title: NB-69 H3K4me1 histone-ChIP-Seq


title: NB-69 H3K4me3 histone-ChIP-Seq


title: NBL-S H3K4me1 histone-ChIP-Seq


title: NBL-S H3K27Ac histone-ChIP-Seq


title: NB-69 H3K27me3 histone-ChIP-Seq


title: KO_CTRL


title: NB-1643 H3K4me3 histone-ChIP-Seq

value: IMDM, 20% FBS, 1% Penicillin/Streptomycin, 2mM L-glutamine


title: NB-1643 Input histone-ChIP-Seq


title: NB-1643 H3K4me1 histone-ChIP-Seq


title: NGP H3K4me3 histone-ChIP-Seq


title: LA-N-5 Input histone-ChIP-Seq


title: NB-1643 H3K27Ac histone-ChIP-Seq


title: LA-N-5 H3K4me3 histone-ChIP-Seq


title: NB-1643 H3K27me3 histone-ChIP-Seq


title: LA-N-5 H3K27me3 histone-ChIP-Seq


title: LA-N-5 H3K4me1 histone-ChIP-Seq


title: LA-N-5 H3K27Ac histone-ChIP-Seq


title: KELLY H3K4me3 histone-ChIP-Seq

value: KELLY


title: KELLY Input histone-ChIP-Seq


title: KELLY H3K27me3 histone-ChIP-Seq


title: KELLY H3K4me1 histone-ChIP-Seq


title: COG-N-415 Input histone-ChIP-Seq

value: IMDM, 20% FBS, 2mM L-glutamine, 1:1000 ITS Premix Supplement


title: COG-N-415 H3K27me3 histone-ChIP-Seq


title: NB-69 H3K27Ac histone-ChIP-Seq


title: COG-N-415 H3K27Ac histone-ChIP-Seq


title: COG-N-415 H3K4me1 histone-ChIP-Seq


title: SKNSH Input ChIP-Seq

data_processing:
FASTQ sequences were adapter and quality trimmed using TrimGalore.
Phred scores were calculated per sample and used during hg19 alignment with bwa samse.
Picard tools was used to remove duplicate reads.
Fragment sizes were estimated using MaSC and these values were used as input into MACS2 for narrow peak calling.
Peaks were called significant using a q-value cut off of 0.05 and results were returned in units of signal per million reads.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

growth_protocol: Cells were grown up to 150 mm plates with the appropriate media.

extract_protocol:
Cells were crosslinked, flash frozen, and sent to Active Motif. According to Active Motif protocol, cells were lysed, sonicated, and then DNA-protein complexes were isolated with antibodies. Samples were reverse-crosslinked and DNA was purified.
Illumina libraries were prepared by Active Motif using standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After 15 cycles of PCR amplification, the resulting DNA libraries were quantified and sequenced on Illumina NextSeq 500.

value: SKNSH

tag: mycn status

value: non-amp


title: SKNSH CMYC ChIP-Seq

value: RPMI 1640, 10% FBS, 1% Penicillin/Streptomycin, 2mM L-Glutamine

value: C-MYC (Santa Cruz N262, #sc-764)


title: COG-N-415 H3K4me3 histone-ChIP-Seq

value: H3K4me3 (Active Motif, #39159)


title: SKNAS Input ChIP-Seq

value: SKNAS


title: NB1643 Input ChIP-Seq

value: amp


title: NB69 CMYC ChIP-Seq


title: NB69 NMYC ChIP-Seq

value: N-MYC (Active Motif, #61185)


title: NB1643 NMYC ChIP-Seq


title: SKNAS CMYC ChIP-Seq


title: LAN5 Input ChIP-Seq


title: NB69 Input ChIP-Seq


title: KELLY Input ChIP-Seq


title: KELLY CMYC ChIP-Seq


title: COGN415 NMYC ChIP-Seq


title: COGN415 Input ChIP-Seq


title: NGP ATAC-Seq REP2

data_processing:
FASTQ sequences were adapter and quality trimmed using TrimGalore.
Phred scores were calculated per sample and used during hg19 alignment with bwa aln for BGI sequences (100 bp reads) and bwa mem for Active Motif sequences (42 bp reads).
Reads with mapping quality <10 were removed. Picard tools v.2.17.9-SNAPSHOT was used to remove duplicates and merge biological replicate BAM files.
MACS2 with --extsize 200 --shift -100  was used for broad peak calling.
Peaks were called significant using a q-value cut off of 0.05 and results were returned in units of signal per million reads.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
N/A
ATAC-libraries of biological replicates were prepared using the protocol documented here: dx.doi.org/10.17504/protocols.io.6r3hd8n


title: KELLY H3K27Ac histone-ChIP-Seq

value: H3K27Ac (Active Motif, #39133)


title: NGP ATAC-Seq REP1


title: NB-69 ATAC-Seq REP2


title: NB-69 ATAC-Seq REP1

value: IMDM, 20% FBS, 1% Penicillin/Streptomycin, 2mM L-Glutamine


title: TCR_HC9

source_name: cerebrospinal fluid derived cells

value: cerebrospinal fluid

value: T cells

value: HC


title: YB4290.24M_B

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

description:
processed data files:
counts.txt.gz
l2tpm.txt.gz

data_processing:
NextSeq using v3 chemistry. Control software version 2.0.12.0, RTA version 1.17.21.3, BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
RNAseq reads aligned with STAR version 2.5.3a and summarized with rsem version 1.3.0
Genome_build: WT.v1.fa.gz
Supplementary_files_format_and_content: phaffii_WT.c2.gtf.gz is a gtf format gene annotation file used to build RSEM index
Supplementary_files_format_and_content: counts.txt.gz are Integer count data per transcript
Supplementary_files_format_and_content: l2tpm.txt.gz are log2 transformed TPM+1 values

organism: Komagataella phaffii

source_name: bulk yeast culture

growth_protocol: BMGY containing 4% (v/v) glycerol was inoculated from a glycerol stock to an initial OD600 of 0.1 in a 24-well culture plate (Corning, Cat. # P-DW10ML24CS) and cultured at ambient temperature and 600 rpm shaking. Samples were collected for sequencing (1) after 24h of biomass accumulation, (2) after pelleting, resuspension, and growth of cells in fresh BMGY for an additional 24h, and (3) after pelleting, resuspension, and growth of cells in BMMY (1.5% v/v methanol) for an additional 24h. These conditions are denoted as (1) 24h glycerol, (2) 48h glycerol, and (3) 24h glycerol + 24h methanol, respectively.

extract_protocol:
Cells were first digested in digestion buffer (50 mM EDTA, 500 mM sorbitol, pH 7.4) supplemented with 0.1% (v/v) 2-Mercaptoethanol and Zymolyase (Zymo Research, Irvine, CA) for 25 min at 30°C and 100 rpm shaking. Lysis and RNA purification was then performed using the RNeasy kit (Qiagen, Cat #74104). RNA quality was analyzed to ensure RNA Quality Number >7.
Non-expressing strain RNA libraries were prepared using the KAPA HyperPrep kit (Roche, Basel, SUI) and sequenced on the Illumina NextSeq platform to generate 40-nucleotide paired-end reads.

tag: strain

value: NRRL YB-4290

tag: culture history

value: 48h methanol


title: YB4290.24M_A


title: YB4290.24G_B

value: 48h glycerol


title: YB4290.0G_C

value: 24h glycerol


title: YB4290.24G_C


title: YB4290.0G_B


title: LAN5 NMYC ChIP-Seq


title: YB4289.24G_B

value: NRRL YB-4289


title: YB4289.24M_A


title: YB4289.24M_B


title: YB4289.24G_C


title: YB4289.24M_C


title: YB4289.24G_A


title: YB378.24M_B

value: NRRL YB-378


title: YB378.24M_A


title: YB4289.0G_A


title: YB4290.0G_A


title: YB4289.0G_C


title: YB4289.0G_B


title: YB4290.24M_C


title: YB378.0G_C


title: YB378.24G_B


title: YB378.24G_C


title: YB378.24G_A


title: YB378.0G_B


title: YB378.0G_A


title: Y7556.24M_C

value: NRRL Y-7556


title: YB4290.24G_A


title: Y7556.24M_B


title: Y7556.24M_A


title: Y7556.0G_C


title: Y7556.24G_C


title: Y7556.24G_A


title: Y7556.0G_A


title: Y7556.0G_B


title: Y48124.24M_C


title: Y48124.24M_B


title: Y48124.24G_D


title: Y48124.24M_A


title: Y48124.0G_A


title: Y48124.0G_B


title: Y48124.0G_C


title: Y48124.24G_A


title: Y48124.24G_B


title: Y48123.24M_D


title: Y48123.24M_C


title: Y48123.24M_B


title: Y48123.24M_A


title: Y48123.0G_B


title: Y48123.24G_B


title: Y48123.0G_C


title: Rv0222Ko-2

city: Shanghai

first: Lin

address: 507 Zhengmin Road

institute: Shanghai Pulmonary Hospital

description:
sample name:
R17025821LR01

data_processing:
Basecalls performed using CASAVA version 1.8
FastQC(version 0.11.2)(Andrews.2010) was used to perform quality control.
RSEM(V1.2.29)(Li B,et al.2011) was applied to analyze gene level expression and isoform level expression.
edgeR(v3.8.5) was used to perform TMM(trimmed mean of M values)(Robinson, M. D., & Oshlack, A. 2010) and CPM(count per million)
Gene Ontology(gene2go.20141211) GenRef(gene_info.20141211) and GENCODE(v19) were used in gene annotation.
Genome_build: mm8
Supplementary_files_format_and_content: excel format

source_name: wild-type C57BL/6 mouse peritoneal macrophages

growth_protocol: Peritoneal macrophages were harvested from mice 3 days after thioglycollate (BD, Sparks, MD) injection.

extract_protocol:
RNA extraction protocol
library construction protocol

treatment_protocol: Macrophages  were either infected with H37Rv or ΔRv0222 (MOI=5) for 4 hours.

tag: cell type

value: Peritoneal macrophages

value: infected with delta_Rv0222 for 4h

tag: moi


title: Rat88_E

city: Miami

first: Ian

last: Hentall

state: FL

address: 1095 NW 14th Terrace

department: Neurological Surgery

institute: University of Miami Miller School of Medicine

data_processing:
FASTQ files were created with the Illumina supplied scripts in the BCL2FASTQ software (v1.8.4)
Illumina adapters trimmed with Trim Galore! v0.4.1
FASTQs aligned to the rn6 reference genome with STAR v2.5.0a using default parameters
--quantMode GeneCounts option in STAR used to count genes against the Ensembl Rnor_6.0.87 GTF annotation file
Genome_build: rn6
Supplementary_files_format_and_content: Processed file is a tab delimited text file indicating the raw counts for each gene in the Ensembl Rnor_6.0.87 GTF file generated with --quantMode GeneCounts option in STAR. A read is counted if it overlaps (1bp or more) with an exon of only one gene on the appropriate strand.

organism: Rattus norvegicus

source_name: spinal cord: cervical thoracic lumbar

extract_protocol:
Immediately after the stimulation period, the spinal cord was rapidly dissected and transversely sectioned into three 0.5 cm blocks encompassing the C4-C6, T7-T9 and L1-L3 spinal segments. The blocks were immediately placed in liquid nitrogen and stored at -80°C. RNA isolated from rat spinal cords was extracted using Trizol and purified using the QIAGEN (Venlo, Netherlands) RNeasy kit, by following the kit’s standard protocol. Samples were analyzed with an Agilent Bioanalyzer (Santa Clara, CA). All analyzed samples passed minimum quality and quantity threshold required for RNA sequencing, including an RNA integrity score (RIN) above 7.0.
Total RNA was prepped for sequencing with the Illumina TruSeq Stranded Total RNA kit with Ribo-Zero depletion according to manufacturer's protocols

tag: tissue

value: spinal cord:cervical thoracic lumbar

value: uninjured, unstimulated


title: Y17741.24M_D


title: Y48123.0G_A


title: Y17741.24M_C


title: H37Rv-2

description:
sample name:
R17025819LR01

value: infected with H37Rv for 4h


title: Rat87_E


title: H37Rv-1

description:
sample name:
R17025818LR01


title: Y17741.24M_B


title: Rat86_E


title: Rat69_E


title: Rat85_E


title: Y17741.24M_A


title: uninfected-2

description:
sample name:
R17025817LR01

value: uninfected


title: Rat76_D

value: injured, stimulated, pimozide 1mg/kg


title: Y17741.24G_D


title: Rat90_C

value: injured, stimulated


title: SK-N-SH ATAC-Seq REP2

value: RPMI 1640, 10% FBS, 1% Penicillin/Streptomycin, 2mM L-Glutamine

value: SK-N-SH


title: uninfected-1

description:
sample name:
R17025816LR01


title: Rat75_D


title: Y17741.24G_B


title: Rat89_C


title: Rv0222Ko-1

description:
sample name:
R17025820LR01


title: Rat95_B

value: injured, untreated


title: SK-N-FI ATAC-Seq REP1

value: SK-N-FI


title: Y17741.0G_C


title: Rat94_B


title: Rat82_A

value: uninjured, untreated


title: Rat83_A


title: SK-N-BE(2)-C ATAC-Seq REP2

description: SKNBE2C.macs2.dnase.broad.SPMR.sorted.bw


title: SK-N-SH ATAC-Seq REP1


title: Y12729.24M_C

value: 48h methanol


title: X33-H14C

data_processing:
Sequence was processed with RTA version 1.18.64 and demultiplexing was done with Broad Technology Labs digital gene expression pipeline
FASTQ files were generated with the bamtofastq function of bedtools 2.26.0
Transcripts were quantified using Salmon (version 0.9.1, Patro et al., 2017) using a modified transcript database consisting of a single K. phaffi transcript per gene each with a 100 nucleotide extension on the 3’ end combined with alpha_GCSF, alpha_hGH and selectable marker transgenes.
Genome_build: phaffiWT_plusTransgenes.fa.gz
Supplementary_files_format_and_content: phaffiWT_plusTransgenes.fa.gz is the modified salmon quantification target
Supplementary_files_format_and_content: counts.txt.gz are Integer count data per transcript
Supplementary_files_format_and_content: l2tpm.txt.gz are log2 transformed TPM+1 values

source_name: bulk yeast cell culture

growth_protocol: BMGY containing 4% (v/v) glycerol was inoculated from a glycerol stock to an initial OD600 of 0.1 in a 24-well culture plate (Corning, Cat. # P-DW10ML24CS, Corning, NY) and cultured at ambient temperature and 600 rpm shaking. After 24h of biomass accumulation, cells were pelleted and resuspended in BMMY, containing 1.5% (v/v) methanol as both a carbon source and for induction of heterologous gene expression, for an additional 24h.

extract_protocol:
Cells were first digested in digestion buffer (50 mM EDTA, 500 mM sorbitol, pH 7.4) supplemented with 0.1% (v/v) 2-Mercaptoethanol and Zymolyase (Zymo Research, Irvine, CA) for 25 min at 30°C and 100 rpm shaking. Lysis and RNA purification was then performed using the RNeasy kit (Qiagen, Cat #74104). RNA quality was analyzed to ensure RNA Quality Number >7.
Protein-expressing strain RNA libraries were prepared using a 3’ DGE method adapted from Soumillon, Cacchiarelli, & Semrau, 2014 and sequenced on an Illumina HiSeq2500 to generate paired reads of 17bp (read1) + 46bp (read2).

tag: protein expressed

value: rhGH

tag: clone id


title: Y17741.0G_B

value: 24h glycerol


title: Rat91_B

tag: treatment


title: Rat84_A


title: SK-N-FI ATAC-Seq REP2


title: Y17741.0G_A


title: Y12729.24M_B


title: X33-H14A


title: X33-H14B


title: X33-H13C


title: Rat93_C


title: Y12729.24M_A


title: X33-H13A


title: SK-N-BE(2)-C ATAC-Seq REP1


title: X33-H13B


title: SK-N-AS ATAC-Seq REP2

value: SK-N-AS


title: Y12729.24G_D

value: 48h glycerol


title: SK-N-AS ATAC-Seq REP1


title: X33-H12C


title: Rat70_A


title: Y12729.24G_B


title: X33-H12A


title: X33-G16C

value: rG-CSF


title: NBL-S ATAC-Seq REP2

value: NBL-S


title: X33-G16A


title: Y12729.24G_A


title: NBL-S ATAC-Seq REP1


title: X33-G13C


title: NB-1643 ATAC-Seq REP2

value: IMDM, 20% FBS, 1% Penicillin/Streptomycin, 2mM L-Glutamine


title: Y12729.0G_B


title: X33-G13B


title: X33-G13A


title: NB-1643 ATAC-Seq REP1


title: NB-1 ATAC-Seq REP2


title: X33-G12A


title: X33-G12B


title: Y12729.0G_A


title: Y11430-H8C


title: Y11430.24M_G


title: X33-G12C


title: X33-H12B


title: NB-1 ATAC-Seq REP1


title: Y11430-H8B


title: Y11430.24M_F


title: LA-N-5 ATAC-Seq REP2


title: Y11430-H8A


title: Y11430-H25C


title: Y11430.24M_E


title: Y11430-H25B


title: Y11430-H25A


title: X33-G16B


title: Y12729.0G_C


title: Y11430.24M_D


title: Y11430-H22C


title: Y11430-H22B


title: KELLY ATAC-Seq REP2

value: KELLY


title: Y11430.24M_C


title: Y11430-H22A


title: Y11430-G16C


title: KELLY ATAC-Seq REP1

value: IMDM, 20% FBS, 1% Penicillin/Streptomycin, 2mM L-glutamine


title: Y11430-G16B


title: Y11430.24M_B


title: Y11430-G13B


title: Y11430-G13C


title: COG-N-440 ATAC-Seq REP2

description: COGN440.macs2.dnase.broad.SPMR.sorted.bw

value: IMDM, 20% FBS, 2mM L-glutamine, 1:1000 ITS Premix Supplement


title: LA-N-5 ATAC-Seq REP1


title: COG-N-453 ATAC-Seq REP2

description: COGN453.macs2.dnase.broad.SPMR.sorted.bw


title: Y11430.24M_A


title: Y11430.24G_D


title: Y11430-G12C


title: Y11430-G12B


title: COG-N-440 ATAC-Seq REP1


title: Y11430-G12A


title: Y11430.24G_B


title: COG-N-415 ATAC-Seq REP2

description: COGN415.macs2.dnase.broad.SPMR.sorted.bw


title: GS115-H14C


title: Y11430.0G_F


title: GS115-H14A


title: GS115-H14B


title: COG-N-415 ATAC-Seq REP1


title: GS115-H13B


title: Y11430.0G_E


title: GS115-H13C


title: Y11430-G16A


title: Y11430.0G_D


title: GS115-H13A


title: COG-N-453 ATAC-Seq REP1


title: 501Mel SiCHD3_3

city: Illkirch-Graffenstaden

first: Guillaume

last: Davidson

address: 1 Rue Laurent Fries

department: Functional Genomics and Cancer

institute: Institut de Genetique et de biologie moleculaire et cellulaire

data_processing:
Image analysis and base calling were performed using RTA 1.18.61 and CASAVA 1.8.2.
Reads were preprocessed in order to remove adapter and low-quality sequences (Phred quality score below 20) using cutadapt version 1.10.
Reads were mapped to rRNA sequences using bowtie version 2.2.8, and reads mapping to rRNA sequences were removed for further analysis. Reads were mapped to spike sequences using bowtie2 version 2.2.8, and reads mapping to spike sequences were removed for further analysis.
Sequence reads were mapped to reference genome hg19 using Tophat v2.0.10 51 and the bowtie2 v2.1.0 aligner. Only uniquely aligned reads were retained for further analyses.
Gene expression quantification was performed from uniquely aligned reads using htseq-count version v0.6.1 with annotations from Ensembl version 75.
Data normalization and quantification of gene expression was performed using the DESeq2 Bioconductor package. Significantly deregulated genes were selected using a log2 fold change >1 and <1 and adjusted p-value cutoff of 0.05.
Genome_build: hg19
Supplementary_files_format_and_content: Excel table (.xls format) containing raw read counts, counts normlalized by library size, counts normalized by both library size and gene length as well as log2(foldchange) and p-values computed by deseq2. The excel table contains two sheets one for the siCHD4 and one for the siCHD3.

source_name: Total RNA: RNA isolation standard procedure (Qiagen kit)

growth_protocol: Melanoma cell line 501Mel was grown in RPMI 1640 medium supplemented with 10% foetal calf serum (FCS).

extract_protocol:
RNA isolation was performed according to standard procedure (Qiagen kit).
Complementary DNA were generated and linearly amplified from 6 ng of total RNA using the Ovation RNA-seq system V2 (NuGEN technologies Inc., Leek, Netherlands), according to manufacturer's instructions. Amplified cDNA was then purified using Agencourt AMPure XP beads (Beckman-Coulter, Villepinte, France) in a 1.8:1 ratio of beads to sample and fragmented by sonication using a Covaris E220 instrument (with duty factor: 10 percent, peak incident power: 175 watts and cycles/burst: 200 for 120 seconds). RNA-Seq libraries were generated from 100 ng of fragmented ds-cDNA using Ovation Ultralow Library System v2 (NuGEN technologies Inc., Leek, Netherlands) according to manufacturer's instructions with only 8 PCR cycles for library amplification. The final libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: SiRNA knockdown experiments were performed with the corresponding ON-TARGET-plus Smart pools purchased from Dharmacon Inc. (Chicago,Il., USA). SiRNAs were transfected using Lipofectamine RNAiMax (Invitrogen, La Jolla, CA, USA) and cells were harvested 72 hours after.

value: Melanoma


title: 501Mel siCHD3_2


title: GS115-H12C


title: Y11430-G13A


title: GS115-H12B


title: 501Mel siCHD3_1


title: GS115-H12A


title: GS115-G14C


title: Y11430.0G_C


title: MCI3

value: blood

value: CD8+ TEMRA cells

tag: diagnosis

value: MCI


title: Y11430.0G_A


title: GS115-G13C


title: Y11430.0G_B


title: 501Mel siCtrl6


title: GS115-G14B


title: GS115-G14A


title: 501Mel siCtrl5


title: GS115-G13A


title: Y11430.24G_C


title: 501Mel siCtrl4


title: X33.0G_C


title: GS115-G12C


title: GS115-G12B


title: 501Mel siCHD4_3


title: X33.0G_A


title: 501Mel siCHD4_2


title: GS115-G12A


title: 501Mel siCHD4_1


title: GS115.24M_B


title: Y48124-H13C


title: GS115.24M_A


title: 501Mel siCtrl3


title: MC__Zf_neg_3

city: Bern

first: Federica Maria

last: Conedera

state: Bern

address: Freiburgstrasse 14

country: Switzerland

institute: Inselspital-University of Bern

data_processing:
The raw reads were first cleaned by removing adapter sequences, trimming low quality ends, and filtering reads with low quality (phred quality <20) using Trimmomatic (Version 0.36) (18). The read alignment was done with STAR (v2.6.0c) (19). As reference we used the Ensembl zebrafish genome build GRCz10 from 2017-06-07 (release 89) and respectively the Ensembl mouse genome build GRCm38.p5 with the gene annotations downloaded on 2018-02-26 from Ensembl (release 91). The STAR alignment options were "--outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50". Gene expression values were computed with the function featureCounts from the R package Rsubread (v1.26.0) (20). The options for featureCounts were: - min mapping quality 10 - min feature overlap 10bp - count multi-mapping reads - count only primary alignments - count reads also if they overlap multiple genes. To detect differentially expressed genes we applied a count based negative binomial model implemented in the software package DESeq2 (R version: 3.5.0, DESeq2 version: 1.20.0). The differential expression was assessed using an exact test adapted for over-dispersed data. Genes showing altered expression with an adjusted p-value < 0.05 (Benjamini and Hochberg method) were considered differentially expressed.
Genome_build: zebrafish genome build GRCz10
Supplementary_files_format_and_content: text files holding gread counts per gene

organism: Danio rerio

extract_protocol:
At different time points after injury induction (Day 1, 3, and 7), both retinas of three gfap:gfap-GFP zebrafish per time point were dissected and kept in cold diethyl pyrocarbonate phosphate buffered saline (DEPC-PBS) (12). Enzymatically dissociation was initiated by 0.05% trypsin (ThermoFisher Scientific) diluted in DEPC-PBS at 37 °C for 10 min. Cell suspension was then mechanically triturated, trypsin inhibitor (10 mg/ml; Sigma-Aldrich) added and the solution centrifuged at 1200 rpm for 5 min. Dissociated retinas were resuspended in DEPC-PBS with 10% FBS and DNase I (200 U/ml; Roche), filtered and collected in Falcon® Round-Bottom Tubes with CellStrainer Cap (12x75 mm; Costar Corning, Cambridge, MA). Hoechst 33342 Ready Flow™ Reagent (ThermoFisher Scientific) was added as a DNA dye for cell cycle analysis. Cells from gfap:gfap-GFP negative siblings were used to determine background fluorescence levels. 100 cells/μl above this threshold were collected from gfap:gfap-GFP positive fish using FACS into separate 96-well plates containing 4 μl lysis buffer comprised of Buffer TCL (1031576; Qiagen) plus 1% 2-mercaptoethanol (63689; Sigma-Aldrich).
After cell sorting, all samples were immediately frozen at −70°C. Sorted cells were processed using the published Smart-seq2 protocol (17) to generate the cDNA libraries. The quality of the RNA, cDNA and final libraries was determined using an Agilent 4200 TapeStation System (Agilent, Santa Clara, CA, USA). The libraries were pooled and sequenced in an Illumina HiSeq2500 (Illumina, San Diego, CA, USA) with a depth of around 20 Mio reads per sample.

treatment_protocol: For the zebrafish, after anesthesia with 0.16 mg/mL ethyl 3-aminobenzoate methanesulfonate salt (Tricaine; Sigma-Aldrich, Buchs, Switzerland) dissolved in the tank water, 1-2 drops of 2% hydroxypropyl methylcellulose (Methocel, OmniVision AG, Neuhausen, Switzerland) were topically applied to the cornea.  A diode laser with a wavelength of 532 nm (Visulas 532s, Carl Zeiss Meditec AG, Oberkochen, Germany) was used to create retinal lesions at the region of the posterior pole around the optic nerve (6). These were confined to the ONL and surrounded by apparently healthy retinal tissue. Four laser burns were applied to the left eye: two superior and two inferior to the optic nerve separated from the nerve by at least two lesion diameters. For the RNAseq analysis, 20 laser burns were created in both eyes. Each burn was produced with 70 mW of power for 100 ms and aimed to have a diameter of 50 µm (6). The right eye was used as internal negative control. To focus the laser-aiming beam on the retina a 2.0 mm laser lens was employed (Ocular Instruments, Bellevue, WA, USA). After laser treatment, fish were revived by placing them in a container with fresh tank water and creating a water flow over the gills.

tag: strain background

value: AB

tag: age

value: 6-9 months

value: retina

value: Muller cells


title: MC__Zf_neg_2


title: GS115-G13B


title: Y48124-H13A

value: rhGH


title: 501Mel siCtrl2


title: GS115.24G_C


title: 501Mel siCtrl1


title: Y48124-H12C


title: X33.0G_B

value: 24h glycerol


title: 501Mel INPUT

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg19 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Peaks were called using MACS 2.1.1.20160309 with ‘--broad’ parameter
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b). Peaks were called with MACS2 and are in broadPeak format.

source_name: Fixed and sonicated chromatin

extract_protocol:
CHD4 ChIP experiments were performed on 0.4% Paraformaldehyde fixed and sonicated chromatin isolated from 501Mel cells according to standard protocols as previously described (Strub et al., 2011).
ChIP-seq libraries were prepared using NEXTflex ChIP-Seq Kit (#5143-02, Bioo Scientific) following the manufacturer's protocol (V12.10) with some modifications. Briefly, 10 ng of ChIP enriched DNA or INPUT DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK, then size selected and cleaned-up using Agencourt AMPure XP beads (#A63881, Beckman). A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded barcoded DNA adapters (NEXTflex ChIP-Seq Barcodes - 6, #514120, Bioo Scientific) using T4 DNA Ligase. The ligated products were enriched by PCR (2 min at 98°C; [30 sec at 98°C, 30 sec at 65°C, 60 sec at 72°C] x 14 cycles; 4 min at 72°C) and cleaned-up using Agencourt AMPure XP beads.


title: Y48124-H12B


title: Y48124-H12A


title: MC__Zf_day7_2

tag: time point

value: 7 day post retinal injury


title: MC__Zf_day7_1


title: 501Mel ChIP CHD4

tag: cell line


title: GS115.0G_B


title: GS115.24M_C

value: 48h methanol


title: Y48124-H13B


title: MC__Zf_neg_1


title: GS115.0G_A


title: Y48124-H11B


title: MC__Zf_day7_3


title: MC__Zf_day3_3

value: 3 day post retinal injury


title: MC__Zf_day3_2


title: Y48124-H11A


title: MC__Zf_day1_2

value: 1 day post retinal injury


title: Y48124-G16C

value: rG-CSF


title: Y48124-H11C


title: MC__Zf_day3_1


title: GS115.0G_C


title: GS115.24G_B

value: 48h glycerol


title: MC__Ms_neg_2

data_processing:
The raw reads were first cleaned by removing adapter sequences, trimming low quality ends, and filtering reads with low quality (phred quality <20) using Trimmomatic (Version 0.36) (18). The read alignment was done with STAR (v2.6.0c) (19). As reference we used the Ensembl zebrafish genome build GRCz10 from 2017-06-07 (release 89) and respectively the Ensembl mouse genome build GRCm38.p5 with the gene annotations downloaded on 2018-02-26 from Ensembl (release 91). The STAR alignment options were "--outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50". Gene expression values were computed with the function featureCounts from the R package Rsubread (v1.26.0) (20). The options for featureCounts were: - min mapping quality 10 - min feature overlap 10bp - count multi-mapping reads - count only primary alignments - count reads also if they overlap multiple genes. To detect differentially expressed genes we applied a count based negative binomial model implemented in the software package DESeq2 (R version: 3.5.0, DESeq2 version: 1.20.0). The differential expression was assessed using an exact test adapted for over-dispersed data. Genes showing altered expression with an adjusted p-value < 0.05 (Benjamini and Hochberg method) were considered differentially expressed.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: text files holding gread counts per gene

extract_protocol:
For RNA-seq experiments using the Rlbp1:GFP mice, retinas were collected in HBSS at different time points (Day 1, 3, and 7) and promptly dissociated as described (13-16). Briefly, both left and right retinas from an adult mouse (in triplicate) were dissected and incubated with papain (Worthington Biochemical, Freehold, NJ, USA) for 10-15 minutes at 37°C. Papain was removed with one wash in HBSS with 10% FBS and DNase I (200 U/ml; Roche), after which retinas were placed in HBSS containing 0.4% BSA (A8806; Sigma-Aldrich) and DNase I (200 U/ml; Roche), dissociated by trituration, passed through a 35 μm cell strainer, and placed on ice. Hoechst 33342 Ready Flow™ Reagent (ThermoFisher Scientific) was added as a DNA dye for cell cycle analysis. Cells from Rlbp1:GFP negative littermates were used to determine background fluorescence levels. 100 cells/μl above this threshold were collected from Rlbp1:GFP positive animals using FACS into separate 96-well plates with 4 μl lysis buffer comprised of Buffer TCL (1031576; Qiagen) plus 1% 2-mercaptoethanol (63689; Sigma-Aldrich).
After cell sorting, all samples were immediately frozen at −70°C. Sorted cells were processed using the published Smart-seq2 protocol (17) to generate the cDNA libraries. The quality of the RNA, cDNA and final libraries was determined using an Agilent 4200 TapeStation System (Agilent, Santa Clara, CA, USA). The libraries were pooled and sequenced in an Illumina HiSeq2500 (Illumina, San Diego, CA, USA) with a depth of around 20 Mio reads per sample.

treatment_protocol: Anesthesia was performed subcutaneously by injecting 45 mg/kg ketamine (Ketalar 50 mg/ml; Orion Pharma AG, Zug, Zurich, Switzerland) and 0.75 mg/kg medetomidine hydrochloride (Domitor, 1 mg/ml; Orion Pharma AG). Pupils were dilated using tropicamide 0.5% and phenylephrine HCl 2.5% (ISPI, Bern, Switzerland). Afterwards, few drops of 2% hydroxypropyl methylcellulose were applied topically to the cornea before the treatment. The same diode laser employed for the zebrafish was used to apply six  laser burns on the left eye: three superior and three inferior to the optic nerve separated from the nerve by at least two lesion diameters. For the RNAseq analysis, 50 laser burns were created in both eyes. Each burn was 100 µm in diameter and produced with 120 mW of power for 60 ms. The right eye was used as internal negative control. After laser damage induction, 0.75 mg/kg atipamezole (Antisedan 5 mg/ml; Orion Pharma AG) was given to reverse anesthesia. Additionally, 200 μL of 0.9% NaCl was injected subcutaneously to prevent dehydration.

value: 4-6 weeks


title: Y48124-G16B


title: MC__Ms_neg_3


title: MC__Zf_day1_3


title: MC__Ms_day7_3


title: MC__Ms_neg_1


title: MC__Ms_day7_2


title: Y48124-G14C


title: X33.24M_B


title: X33.24M_C


title: MC__Ms_day3_3


title: MC__Ms_day7_1


title: MC__Ms_day3_2


title: Y48124-G14B


title: Y48124-G14A


title: Y48124-G13C


title: MC__Zf_day1_1


title: MC__Ms_day1_3


title: MC__Ms_day3_1


title: Y48124-G13A


title: X33.24G_B


title: X33.24G_C


title: MC__Ms_day1_2


title: X33.24G_A


title: Y48124-G16A


title: MC__Ms_day1_1


title: X33.24M_A


title: Y48124-G13B


title: Non-SCCB5

status: Public on Nov 02 2019

city: Los Angeles

first: Liang

state: CA

address: 675 Charles E Young Dr

department: MIMG

institute: UCLA

data_processing:
Raw reads were mapped to hg38 human genome using TOIL
Transcripts were quantified by expectation-maximization (RSEM), TPM was calculated
Gene list was filtered for HUGO coding genes
Supplementary_files_format_and_content: TPM-HUGO-FFPE.txt: the TPM matrix for clinical samples; TPM-HUGO-Bladder-PARCB.txt: the TPM  matrix for Bladder-PARCB cell lines

source_name: Clinical Non-SCCB sample

growth_protocol: For bladder-PARCB cell lines, cells were cultured in stem cell culture medium in regular tissue culture flask. The cells grow in suspension condition.

extract_protocol:
For clinical samples, using Ambion RecoverAll kit (Thermofisher, #AM1975); For Bladder-PARCB cells, using Qiagen miRNeasy kit (Qiagen, #217004)
Human FFPE RNA-seq kit (Nugen, #0341-32)

value: Non-SCCB (urothelial carcinoma)

tag: sample type

value: Archived FFPE samples


title: SCCB6

source_name: Clinical SCCB sample

value: SCCB


title: Non-SCCB6


title: SCCB7


title: SCCB9


title: Non-SCCB3


title: Non-SCCB4


title: Bladder-PARCB2

source_name: Genetically engineered SCCB cell line

value: SCCB cell line

value: Transformed human primary urothelial cells

value: PARCB


title: NB3_AS601245_C1D2_rep4_24h

city: Mölndal

first: Ramy

last: Elgendy

state: Göteborg

address: Pepparedsleden 1

institute: AstraZeneca

data_processing:
Illumina Sequencing by HiSeq3000
Sequenced reads were quality-controlled, trimmed for adaptor sequences (if present), then mapped to the ENSEMBL GRCh38 reference genome using STAR v 2.6.0a
Uniquely-mapped reads aligned to exons were counted by HTSeq v.0.6.1.
The raw read counts were normalized by the DESeq2 R package v.3.4.4
Genome_build: GRCh38 (ftp://ftp.ensembl.org/pub/release-92/fasta/homo_sapiens/dna/), downloaded on July 2nd, 2018.
Supplementary_files_format_and_content: Tab-delimited text files include raw counts of sequencing reads for each Sample

source_name: Neural crest-derived cells

growth_protocol: Cells were cultured in 3 parts DMEM Low glucose, pyruvate GlutaMax medium (ThermoFisher, cat. 21885-025) and 1 part Ham’s F12 Nutrient Mix (ThermoFisher, cat. 31765-027), supplemented with 10% B-27 (ThermoFisher, cat. 17504044) and 1% penicillin-streptomycin mix.

extract_protocol:
After the treatment, the drug-containing medium was removed and the plates were snap frozen on dry ice. RNA isolation and cDNA synthesis were performed by the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Takara Bio USA), as per the manufacturer's instructions.
RNA libraries were prepared for sequencing using the SMART-Seq2 method.

treatment_protocol: Cells were seeded in 384-well plates (1500 cells/well) and treated with 13 different chemical componds (3 doses and 4 replicates each).

value: Human-derived xenograft neuroblastoma (NB) primary cells

tag: passages

value: Child

tag: cell line id

tag: chemical compound


title: Non-SCCB9


title: Non-SCCB1


title: Non-SCCB8


title: Bladder-PARCB1


title: Non-SCCB10


title: Non-SCCB7


title: SCCB8


title: Non-SCCB2


title: SCCB5


title: SMYD2

city: Tianjin

first: Yan

address: #22 Qixiangtai Road

department: Department of Biochemistry and Molecular Biology

institute: Tianjin Medical University

description: Chip-chip MDA-MB-231 cells SMYD2

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Raw data were extracted as pair files by NimbleScan software. We performed Median-centering, quantile normalization, and linear smoothing by Bioconductor packages Ringo, limma and MEDME. After normalization, a normalized log2-ratio data was created for each sample. From the normalized log2-ratio data, a permutation-based peak-finding algorithm provided by NimbleScan v2.5 (Roche-NimbleGen) was applied to find peaks which represent significant positive enrichment. NimbleScan detects peaks by searching for 4 or more probes whose signals were above the specified cutoff values, ranging from 90% to 15%, using a 500bp sliding window. The cutoff values are a percentage of a hypothetical maximum, which is the mean + 6[standard deviation]. The ratio data is then randomized 20 times to evaluate the probability of “false positives”.

source_name: SMYD2 ChIP DNA from MDA-MB-231 cells

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

extract_protocol: 1x10E7 cells were washed twice with PBS and cross-linked with 1% formaldehyde at room temperature for 10 min. Cells then were rinsed with ice-cold PBS twice and collected into 100 mM Tris-HCl (pH 9.4), 10 mM DTT and incubated for 15 min at 30°C and centrifuged for 5 min at 2000 g. Cells were washed sequentially with 1 ml of ice-cold PBS, buffer I (0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 10 mM HEPES, pH 6.5), and buffer II (200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10 mM HEPES, pH 6.5). Cells were then resuspended in 0.3 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.1, 1× protease inhibitor cocktail (Roche Molecular Biochemicals, Indianapolis, IN) and sonicated three times for 10 s each at the maximum setting (Fisher Sonic Dismembrator, Model 300) followed by centrifugation for 10 min. Supernatants were collected and diluted in buffer (1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris-HCl, pH 8.1) followed by immunoclearing with 2 μg sheared salmon sperm DNA, 20 μl preimmune serum and protein A-sepharose (45 μl of 50% slurry in 10 mM Tris-HCl, pH 8.1, 1 mM EDTA) for 2 hr at 4°C. Immunoprecipitation was performed for 6 hr or overnight at 4°C with specific antibodies. After immunoprecipitation, 45 μl protein A-Sepharose and 2 μg of salmon sperm DNA were added and the incubation was continued for another 1 hr. Precipitates were washed sequentially for 10 min each in TSE I (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 150 mM NaCl), TSE II (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl, pH 8.1, 500 mM NaCl), and buffer III (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl, pH 8.1). Precipitates were then washed three times with TE buffer and extracted three times with 1% SDS, 0.1 M NaHCO3. Eluates were pooled and heated at 65°C for at least 6 hr to reverse the formaldehyde cross-linking. DNA fragments were purified with a QIAquick Spin Kit (Qiagen, CA). For PCR, 1 μl from a 50 μl DNA extraction and 21–25 cycles of amplification were used.

treatment_protocol: 1x10E7 cells were collected for ChIP assay per antibody

value: MDA-MB-231 cells

tag: chip antibody

source_name: Input DNA from MDA-MB-231 cells

growth_protocol: MDA-MB-231 cell lines were maintained in Dulbecco's modified Eagle's medium (DMEM) (Gibco, Invitrogen). All media contained 10% fetal bovine serum (FBS), 100 units/ml penicillin, and 100 mg/ml streptomycin (Gibco BRL).

value: none, input DNA


title: NB3_Control_CTR_rep16_24h

value: Control


title: NB3_AS601245_C1D1_rep4_24h


title: SCCB1


title: SCCB2


title: NB3_AZDS438_C2D2_rep4_24h


title: SCCB4


title: SCCB3


title: EZH2

description: Chip-chip MDA-MB-231 cells EZH2

source_name: EZH2 ChIP DNA from MDA-MB-231 cells

growth_protocol: MDA-MB-231 cell lines were maintained in Dulbecco's modified Eagle's medium (DMEM) (Gibco, Invitrogen). All media contained 10% fetal bovine serum (FBS),


title: NB3_AS601245_C1D3_rep4_24h


title: NB3_AZDS438_C2D3_rep4_24h


title: NB3_AZDS438_C2D1_rep4_24h


title: NB3_DL-PDMP_C3D2_rep4_24h

value: DL-PDMP


title: NB3_DL-PDMP_C3D1_rep4_24h


title: NB3_DMSO1_DMSO1_rep10_24h

value: DMSO


title: NB3_Fasudil_C4D1_rep4_24h

value: Fasudil


title: NB2_DMSO1_DMSO1_rep10_24h


title: NB2_Torin 2_C13D2_rep4_24h

value: Torin 2


title: NB2_DMSO2_DMSO2_rep8_24h


title: NB2_Rosiglitazone_C12D3_rep4_24h

value: Rosiglitazone


title: NB2_Torin 2_C13D3_rep4_24h


title: NB3_GW405833_C5D1_rep4_24h


title: NB3_Fasudil_C4D2_rep4_24h


title: NB2_Torin 2_C13D1_rep4_24h


title: NB3_Control_CTR_rep15_24h


title: NB3_Fasudil_C4D3_rep4_24h


title: NB3_GW405833_C5D2_rep4_24h


title: NB2_Rosiglitazone_C12D2_rep4_24h


title: NB3_GW405833_C5D3_rep4_24h


title: NB3_JQ1_C6D2_rep4_24h


title: NB3_JQ1_C6D1_rep4_24h


title: NB2_Control_CTR_rep16_24h


title: NB2_Rosiglitazone_C12D1_rep4_24h


title: NB3_Lovastatin_C7D1_rep4_24h

value: Lovastatin


title: NB3_DMSO2_DMSO2_rep10_24h


title: NB3_Lovastatin_C7D2_rep4_24h


title: NB2_DMSO1_DMSO1_rep8_24h


title: NB2_DMSO2_DMSO2_rep10_24h


title: NB2_DMSO2_DMSO2_rep9_24h


title: NB2_Retinoic acid_C11D3_rep4_24h

value: Retinoic acid


title: NB2_PK11195_C10D3_rep4_24h


title: NB3_JQ1_C6D3_rep4_24h


title: NB2_Retinoic acid_C11D1_rep4_24h


title: NB2_Retinoic acid_C11D2_rep4_24h


title: NB2_PK11195_C10D2_rep4_24h


title: NB2_Palbociclib_C9D3_rep4_24h

value: Palbociclib


title: NB3_Control_CTR_rep14_24h


title: NB2_PK11195_C10D1_rep4_24h


title: NB2_Omiplasib_C8D3_rep4_24h

value: Omiplasib


title: NB2_Control_CTR_rep15_24h


title: NB2_Palbociclib_C9D2_rep4_24h


title: NB3_Lovastatin_C7D3_rep4_24h


title: NB2_Palbociclib_C9D1_rep4_24h


title: NB3_Omiplasib_C8D2_rep4_24h


title: NB3_Omiplasib_C8D3_rep4_24h


title: NB3_PK11195_C10D3_rep4_24h


title: NB3_DMSO1_DMSO1_rep9_24h


title: NB3_PK11195_C10D2_rep4_24h


title: NB3_Palbociclib_C9D3_rep4_24h


title: NB3_Palbociclib_C9D2_rep4_24h


title: NB3_Palbociclib_C9D1_rep4_24h


title: NB2_DMSO2_DMSO2_rep7_24h


title: NB2_Lovastatin_C7D3_rep4_24h


title: NB2_Omiplasib_C8D2_rep4_24h


title: NB2_Lovastatin_C7D2_rep4_24h


title: NB2_JQ1_C6D2_rep4_24h


title: NB2_JQ1_C6D1_rep4_24h


title: NB2_JQ1_C6D3_rep4_24h


title: NB2_Lovastatin_C7D1_rep4_24h


title: NB3_Omiplasib_C8D1_rep4_24h


title: NB2_DMSO1_DMSO1_rep9_24h


title: NB3_PK11195_C10D1_rep4_24h


title: NB2_GW405833_C5D2_rep4_24h


title: NB3_Retinoic acid_C11D2_rep4_24h


title: NB2_Control_CTR_rep14_24h


title: NB3_Rosiglitazone_C12D1_rep4_24h


title: NB2_GW405833_C5D3_rep4_24h


title: NB3_Retinoic acid_C11D3_rep4_24h


title: NB3_Retinoic acid_C11D1_rep4_24h


title: NB3_Rosiglitazone_C12D2_rep4_24h


title: NB3_Control_CTR_rep13_24h


title: NB3_Torin 2_C13D1_rep4_24h


title: NB3_AS601245_C1D1_rep3_24h


title: NB3_Torin 2_C13D2_rep4_24h


title: NB3_Rosiglitazone_C12D3_rep4_24h


title: NB2_DMSO1_DMSO1_rep7_24h


title: NB3_Torin 2_C13D3_rep4_24h


title: NB2_GW405833_C5D1_rep4_24h


title: NB2_Fasudil_C4D3_rep4_24h


title: NB3_DMSO2_DMSO2_rep9_24h


title: NB2_Fasudil_C4D1_rep4_24h


title: NB3_DL-PDMP_C3D3_rep4_24h


title: NB2_Omiplasib_C8D1_rep4_24h


title: NB2_DL-PDMP_C3D3_rep4_24h


title: NB2_AZDS438_C2D3_rep4_24h


title: NB2_DL-PDMP_C3D2_rep4_24h


title: NB2_DL-PDMP_C3D1_rep4_24h


title: NB3_Control_CTR_rep12_24h


title: NB2_AZDS438_C2D2_rep4_24h


title: NB2_AZDS438_C2D1_rep4_24h


title: NB2_Control_CTR_rep13_24h


title: NB3_AS601245_C1D2_rep3_24h


title: NB3_AZDS438_C2D2_rep3_24h


title: NB3_AS601245_C1D3_rep3_24h


title: NB3_AZDS438_C2D1_rep3_24h


title: NB3_AZDS438_C2D3_rep3_24h


title: NB3_DMSO1_DMSO1_rep8_24h


title: NB2_Fasudil_C4D2_rep4_24h


title: NB3_Fasudil_C4D2_rep3_24h


title: NB2_AS601245_C1D1_rep4_24h


title: NB2_AS601245_C1D3_rep4_24h


title: NB2_AS601245_C1D2_rep4_24h


title: NB2_Torin 2_C13D3_rep3_24h


title: NB2_Rosiglitazone_C12D3_rep3_24h


title: NB2_Rosiglitazone_C12D2_rep3_24h


title: NB2_Torin 2_C13D2_rep3_24h


title: NB2_Torin 2_C13D1_rep3_24h


title: NB3_DL-PDMP_C3D1_rep3_24h


title: NB3_DL-PDMP_C3D2_rep3_24h


title: NB2_Control_CTR_rep12_24h


title: NB3_GW405833_C5D2_rep3_24h


title: NB2_Rosiglitazone_C12D1_rep3_24h


title: NB3_GW405833_C5D3_rep3_24h


title: NB3_GW405833_C5D1_rep3_24h


title: NB3_Fasudil_C4D3_rep3_24h


title: NB3_Control_CTR_rep11_24h


title: NB3_Fasudil_C4D1_rep3_24h


title: NB3_JQ1_C6D2_rep3_24h


title: NB3_Lovastatin_C7D2_rep3_24h


title: NB2_DMSO2_DMSO2_rep6_24h


title: NB3_JQ1_C6D3_rep3_24h


title: NB3_DL-PDMP_C3D3_rep3_24h


title: NB3_Lovastatin_C7D1_rep3_24h


title: NB3_JQ1_C6D1_rep3_24h


title: NB3_DMSO2_DMSO2_rep8_24h


title: NB2_DMSO1_DMSO1_rep6_24h


title: NB2_Retinoic acid_C11D2_rep3_24h


title: NB2_Retinoic acid_C11D1_rep3_24h


title: NB2_PK11195_C10D2_rep3_24h


title: NB2_PK11195_C10D1_rep3_24h


title: NB3_Lovastatin_C7D3_rep3_24h


title: NB2_Retinoic acid_C11D3_rep3_24h


title: NB2_Palbociclib_C9D1_rep3_24h


title: NB2_Palbociclib_C9D2_rep3_24h


title: NB2_Palbociclib_C9D3_rep3_24h


title: NB2_Omiplasib_C8D2_rep3_24h


title: NB3_Control_CTR_rep10_24h


title: NB3_Omiplasib_C8D3_rep3_24h


title: NB3_Omiplasib_C8D2_rep3_24h


title: NB2_Omiplasib_C8D3_rep3_24h


title: NB3_Palbociclib_C9D1_rep3_24h


title: NB3_Retinoic acid_C11D1_rep3_24h


title: NB3_PK11195_C10D2_rep3_24h


title: NB2_Control_CTR_rep11_24h


title: NB3_Palbociclib_C9D2_rep3_24h


title: NB3_Omiplasib_C8D1_rep3_24h


title: NB3_Palbociclib_C9D3_rep3_24h


title: NB2_DMSO2_DMSO2_rep5_24h


title: NB3_DMSO1_DMSO1_rep7_24h


title: NB2_PK11195_C10D3_rep3_24h


title: NB2_Lovastatin_C7D2_rep3_24h


title: NB2_JQ1_C6D3_rep3_24h


title: NB2_Lovastatin_C7D3_rep3_24h


title: NB3_PK11195_C10D1_rep3_24h


title: NB2_Lovastatin_C7D1_rep3_24h


title: NB2_Omiplasib_C8D1_rep3_24h


title: NB2_JQ1_C6D2_rep3_24h


title: NB2_GW405833_C5D3_rep3_24h


title: NB3_PK11195_C10D3_rep3_24h


title: NB2_Control_CTR_rep10_24h


title: NB3_Control_CTR_rep9_24h


title: NB3_Rosiglitazone_C12D1_rep3_24h


title: NB3_Torin 2_C13D2_rep3_24h


title: NB2_GW405833_C5D1_rep3_24h


title: NB3_Rosiglitazone_C12D2_rep3_24h


title: NB3_Torin 2_C13D3_rep3_24h


title: NB3_Retinoic acid_C11D2_rep3_24h


title: NB3_AS601245_C1D1_rep2_24h


title: NB3_Rosiglitazone_C12D3_rep3_24h


title: NB3_Torin 2_C13D1_rep3_24h


title: NB3_AS601245_C1D2_rep2_24h


title: NB2_JQ1_C6D1_rep3_24h


title: NB2_Fasudil_C4D3_rep3_24h


title: NB2_Fasudil_C4D2_rep3_24h


title: NB2_DMSO1_DMSO1_rep5_24h


title: NB2_GW405833_C5D2_rep3_24h


title: NB3_Retinoic acid_C11D3_rep3_24h


title: NB2_DL-PDMP_C3D2_rep3_24h


title: NB2_AZDS438_C2D2_rep3_24h


title: NB2_DL-PDMP_C3D3_rep3_24h


title: NB2_Fasudil_C4D1_rep3_24h


title: NB2_DL-PDMP_C3D1_rep3_24h


title: NB3_Control_CTR_rep8_24h


title: NB2_Control_CTR_rep9_24h


title: NB2_AZDS438_C2D1_rep3_24h


title: NB2_AZDS438_C2D3_rep3_24h


title: NB2_AS601245_C1D3_rep3_24h


title: NB3_AS601245_C1D3_rep2_24h


title: NB3_DMSO2_DMSO2_rep7_24h


title: NB3_AZDS438_C2D1_rep2_24h


title: NB3_AZDS438_C2D3_rep2_24h


title: NB3_AZDS438_C2D2_rep2_24h


title: NB3_DL-PDMP_C3D1_rep2_24h


title: NB3_Fasudil_C4D2_rep2_24h


title: NB3_Fasudil_C4D1_rep2_24h


title: NB3_DMSO1_DMSO1_rep6_24h


title: NB3_Fasudil_C4D3_rep2_24h


title: NB2_Torin 2_C13D3_rep2_24h


title: NB2_Rosiglitazone_C12D2_rep2_24h


title: NB2_Rosiglitazone_C12D1_rep2_24h


title: NB2_Torin 2_C13D2_rep2_24h


title: NB3_DL-PDMP_C3D3_rep2_24h


title: NB2_Retinoic acid_C11D3_rep2_24h


title: NB2_Rosiglitazone_C12D3_rep2_24h


title: NB2_Retinoic acid_C11D2_rep2_24h


title: NB3_DL-PDMP_C3D2_rep2_24h


title: NB2_AS601245_C1D1_rep3_24h


title: NB3_GW405833_C5D1_rep2_24h


title: NB3_Control_CTR_rep7_24h


title: NB3_GW405833_C5D2_rep2_24h


title: NB2_Control_CTR_rep8_24h


title: NB2_DMSO2_DMSO2_rep4_24h


title: NB2_AS601245_C1D2_rep3_24h


title: NB3_GW405833_C5D3_rep2_24h


title: NB3_JQ1_C6D2_rep2_24h


title: NB2_Torin 2_C13D1_rep2_24h


title: NB3_Lovastatin_C7D1_rep2_24h


title: NB3_JQ1_C6D3_rep2_24h


title: NB3_Lovastatin_C7D2_rep2_24h


title: NB3_Lovastatin_C7D3_rep2_24h


title: NB3_Omiplasib_C8D1_rep2_24h


title: NB2_DMSO1_DMSO1_rep4_24h


title: NB3_DMSO2_DMSO2_rep6_24h


title: NB2_Retinoic acid_C11D1_rep2_24h


title: NB2_PK11195_C10D2_rep2_24h


title: NB2_Omiplasib_C8D1_rep2_24h


title: NB2_Omiplasib_C8D3_rep2_24h


title: NB2_Omiplasib_C8D2_rep2_24h


title: NB3_PK11195_C10D1_rep2_24h


title: NB2_Control_CTR_rep7_24h


title: NB3_PK11195_C10D2_rep2_24h


title: NB3_Palbociclib_C9D3_rep2_24h


title: NB3_Omiplasib_C8D2_rep2_24h


title: NB3_Control_CTR_rep6_24h


title: NB3_PK11195_C10D3_rep2_24h


title: NB2_Palbociclib_C9D1_rep2_24h


title: NB3_Palbociclib_C9D2_rep2_24h


title: NB3_JQ1_C6D1_rep2_24h


title: NB3_Retinoic acid_C11D1_rep2_24h


title: NB2_DMSO2_DMSO2_rep3_24h


title: NB3_DMSO1_DMSO1_rep5_24h


title: NB2_Lovastatin_C7D3_rep2_24h


title: NB2_PK11195_C10D3_rep2_24h


title: NB2_Palbociclib_C9D2_rep2_24h


title: NB2_PK11195_C10D1_rep2_24h


title: NB2_Palbociclib_C9D3_rep2_24h


title: NB2_Lovastatin_C7D1_rep2_24h


title: NB2_JQ1_C6D2_rep2_24h


title: NB3_Omiplasib_C8D3_rep2_24h


title: NB2_GW405833_C5D3_rep2_24h


title: NB3_Palbociclib_C9D1_rep2_24h


title: NB3_Retinoic acid_C11D2_rep2_24h


title: NB2_GW405833_C5D1_rep2_24h


title: NB3_Control_CTR_rep5_24h


title: NB2_JQ1_C6D1_rep2_24h


title: NB3_Retinoic acid_C11D3_rep2_24h


title: NB2_Control_CTR_rep6_24h


title: NB3_Torin 2_C13D2_rep2_24h


title: NB3_AS601245_C1D3_rep1_24h


title: NB3_Rosiglitazone_C12D3_rep2_24h


title: NB3_AS601245_C1D1_rep1_24h


title: NB3_Rosiglitazone_C12D2_rep2_24h


title: NB2_Fasudil_C4D3_rep2_24h


title: NB3_Torin 2_C13D1_rep2_24h


title: NB3_DMSO2_DMSO2_rep5_24h


title: NB3_AS601245_C1D2_rep1_24h


title: NB2_JQ1_C6D3_rep2_24h


title: NB2_Fasudil_C4D2_rep2_24h


title: NB2_Fasudil_C4D1_rep2_24h


title: NB2_DL-PDMP_C3D3_rep2_24h


title: NB2_GW405833_C5D2_rep2_24h


title: NB2_DL-PDMP_C3D2_rep2_24h


title: NB2_DL-PDMP_C3D1_rep2_24h


title: NB2_AZDS438_C2D3_rep2_24h


title: NB2_AZDS438_C2D2_rep2_24h


title: NB2_AS601245_C1D3_rep2_24h


title: NB3_Rosiglitazone_C12D1_rep2_24h


title: NB3_Torin 2_C13D3_rep2_24h


title: NB2_AS601245_C1D2_rep2_24h


title: NB2_Control_CTR_rep5_24h


title: NB3_AZDS438_C2D1_rep1_24h


title: NB3_AZDS438_C2D2_rep1_24h


title: NB3_Control_CTR_rep4_24h


title: NB2_DMSO1_DMSO1_rep3_24h


title: NB3_DL-PDMP_C3D1_rep1_24h


title: NB3_Fasudil_C4D3_rep1_24h


title: NB3_GW405833_C5D1_rep1_24h


title: NB3_Fasudil_C4D1_rep1_24h


title: NB3_Fasudil_C4D2_rep1_24h


title: NB3_DL-PDMP_C3D2_rep1_24h


title: NB3_DL-PDMP_C3D3_rep1_24h


title: NB3_DMSO1_DMSO1_rep4_24h


title: NB2_Torin 2_C13D3_rep1_24h


title: NB2_AS601245_C1D1_rep2_24h


title: NB2_Torin 2_C13D2_rep1_24h


title: NB2_Torin 2_C13D1_rep1_24h


title: NB2_AZDS438_C2D1_rep2_24h


title: NB2_Rosiglitazone_C12D3_rep1_24h


title: NB2_Rosiglitazone_C12D2_rep1_24h


title: NB2_Retinoic acid_C11D1_rep1_24h


title: NB2_Retinoic acid_C11D3_rep1_24h


title: NB3_GW405833_C5D2_rep1_24h


title: NB3_AZDS438_C2D3_rep1_24h


title: NB2_Control_CTR_rep4_24h


title: NB3_Control_CTR_rep3_24h


title: NB2_Retinoic acid_C11D2_rep1_24h


title: NB3_GW405833_C5D3_rep1_24h


title: NB2_Lovastatin_C7D2_rep2_24h


title: NB3_JQ1_C6D3_rep1_24h


title: NB3_JQ1_C6D1_rep1_24h


title: NB3_JQ1_C6D2_rep1_24h


title: NB2_DMSO2_DMSO2_rep2_24h


title: NB3_Lovastatin_C7D1_rep1_24h


title: NB3_Omiplasib_C8D2_rep1_24h


title: NB2_PK11195_C10D3_rep1_24h


title: NB3_Lovastatin_C7D2_rep1_24h


title: NB2_DMSO1_DMSO1_rep2_24h


title: NB3_DMSO2_DMSO2_rep4_24h


title: NB2_PK11195_C10D2_rep1_24h


title: NB2_PK11195_C10D1_rep1_24h


title: NB3_Omiplasib_C8D1_rep1_24h


title: NB2_Palbociclib_C9D2_rep1_24h


title: NB2_Palbociclib_C9D3_rep1_24h


title: NB2_Rosiglitazone_C12D1_rep1_24h


title: NB2_Omiplasib_C8D2_rep1_24h


title: NB2_Omiplasib_C8D1_rep1_24h


title: NB2_Control_CTR_rep3_24h


title: NB2_Lovastatin_C7D3_rep1_24h


title: NB2_Omiplasib_C8D3_rep1_24h


title: NB3_Omiplasib_C8D3_rep1_24h


title: NB3_Palbociclib_C9D1_rep1_24h


title: NB3_Lovastatin_C7D3_rep1_24h


title: NB2_Palbociclib_C9D1_rep1_24h


title: NB3_Control_CTR_rep2_24h


title: NB3_Palbociclib_C9D3_rep1_24h


title: NB3_PK11195_C10D2_rep1_24h


title: NB3_Palbociclib_C9D2_rep1_24h


title: NB3_PK11195_C10D3_rep1_24h


title: NB3_PK11195_C10D1_rep1_24h


title: NB3_Retinoic acid_C11D1_rep1_24h


title: NB3_Retinoic acid_C11D3_rep1_24h


title: NB3_Retinoic acid_C11D2_rep1_24h


title: NB2_DMSO2_DMSO2_rep1_24h


title: NB3_DMSO1_DMSO1_rep3_24h


title: NB2_JQ1_C6D1_rep1_24h


title: NB2_GW405833_C5D3_rep1_24h


title: NB2_JQ1_C6D2_rep1_24h


title: NB2_Lovastatin_C7D1_rep1_24h


title: NB2_JQ1_C6D3_rep1_24h


title: NB2_Lovastatin_C7D2_rep1_24h


title: NB2_GW405833_C5D1_rep1_24h


title: NB2_Fasudil_C4D3_rep1_24h


title: NB2_Fasudil_C4D2_rep1_24h


title: NB2_Control_CTR_rep2_24h


title: NB3_Control_CTR_rep1_24h


title: NB3_Rosiglitazone_C12D2_rep1_24h


title: NB3_Rosiglitazone_C12D3_rep1_24h


title: NB3_Torin 2_C13D1_rep1_24h


title: NB3_Torin 2_C13D2_rep1_24h


title: NB3_Torin 2_C13D3_rep1_24h


title: NB3_DMSO2_DMSO2_rep3_24h


title: NB3_DMSO2_DMSO2_rep2_24h


title: NB3_DMSO1_DMSO1_rep2_24h


title: NB3_DMSO1_DMSO1_rep1_24h


title: NB3_DMSO2_DMSO2_rep1_24h


title: NB2_DMSO1_DMSO1_rep1_24h


title: NB2_DL-PDMP_C3D2_rep1_24h


title: NB2_DL-PDMP_C3D3_rep1_24h


title: NB2_GW405833_C5D2_rep1_24h


title: NB2_AZDS438_C2D1_rep1_24h


title: NB2_AS601245_C1D3_rep1_24h


title: NB2_DL-PDMP_C3D1_rep1_24h


title: NB2_AZDS438_C2D2_rep1_24h


title: NB2_AS601245_C1D2_rep1_24h


title: NB3_Control_CTR_rep16_6h


title: NB2_AZDS438_C2D3_rep1_24h


title: NB3_AS601245_C1D2_rep4_6h


title: NB2_Control_CTR_rep1_24h


title: NB3_AS601245_C1D1_rep4_6h


title: NB3_AZDS438_C2D1_rep4_6h


title: NB3_AS601245_C1D3_rep4_6h


title: NB2_AS601245_C1D1_rep1_24h


title: NB3_Rosiglitazone_C12D1_rep1_24h


title: NB3_AZDS438_C2D2_rep4_6h


title: NB2_Fasudil_C4D1_rep1_24h


title: NB3_Fasudil_C4D1_rep4_6h


title: NB3_DL-PDMP_C3D2_rep4_6h


title: NB3_DL-PDMP_C3D1_rep4_6h


title: NB3_DL-PDMP_C3D3_rep4_6h


title: NB3_AZDS438_C2D3_rep4_6h


title: NB3_DMSO1_DMSO1_rep10_6h


title: NB2_DMSO1_DMSO1_rep10_6h


title: NB2_DMSO1_DMSO1_rep9_6h


title: NB2_DMSO2_DMSO2_rep10_6h


title: NB2_Torin 2_C13D3_rep4_6h


title: NB2_DMSO2_DMSO2_rep8_6h


title: NB2_Torin 2_C13D2_rep4_6h


title: NB2_Rosiglitazone_C12D1_rep4_6h


title: NB3_Control_CTR_rep15_6h


title: NB2_Rosiglitazone_C12D2_rep4_6h


title: NB3_Fasudil_C4D2_rep4_6h


title: NB3_GW405833_C5D1_rep4_6h


title: NB2_Rosiglitazone_C12D3_rep4_6h


title: NB3_GW405833_C5D2_rep4_6h


title: NB2_Torin 2_C13D1_rep4_6h


title: NB3_JQ1_C6D1_rep4_6h


title: NB2_Control_CTR_rep16_6h


title: NB3_JQ1_C6D2_rep4_6h


title: NB3_Lovastatin_C7D1_rep4_6h


title: NB2_DMSO2_DMSO2_rep9_6h


title: NB3_GW405833_C5D3_rep4_6h


title: NB3_DMSO2_DMSO2_rep10_6h


title: NB3_JQ1_C6D3_rep4_6h


title: NB2_Retinoic acid_C11D3_rep4_6h


title: NB3_Lovastatin_C7D2_rep4_6h


title: NB2_DMSO1_DMSO1_rep8_6h


title: NB2_Retinoic acid_C11D1_rep4_6h


title: NB3_Fasudil_C4D3_rep4_6h


title: NB2_PK11195_C10D3_rep4_6h


title: NB2_Retinoic acid_C11D2_rep4_6h


title: NB2_PK11195_C10D2_rep4_6h


title: NB2_PK11195_C10D1_rep4_6h


title: NB2_Palbociclib_C9D2_rep4_6h


title: NB2_Palbociclib_C9D1_rep4_6h


title: NB2_Palbociclib_C9D3_rep4_6h


title: NB2_Omiplasib_C8D3_rep4_6h


title: NB3_Omiplasib_C8D2_rep4_6h


title: NB3_Lovastatin_C7D3_rep4_6h


title: NB3_Omiplasib_C8D1_rep4_6h


title: NB3_Palbociclib_C9D3_rep4_6h


title: NB3_PK11195_C10D2_rep4_6h


title: NB3_PK11195_C10D1_rep4_6h


title: NB3_PK11195_C10D3_rep4_6h


title: NB3_Omiplasib_C8D3_rep4_6h


title: NB2_DMSO2_DMSO2_rep7_6h


title: NB2_Lovastatin_C7D2_rep4_6h


title: NB2_Lovastatin_C7D1_rep4_6h


title: NB2_Omiplasib_C8D2_rep4_6h


title: NB2_JQ1_C6D2_rep4_6h


title: NB3_Palbociclib_C9D2_rep4_6h


title: NB2_Control_CTR_rep14_6h


title: NB2_GW405833_C5D2_rep4_6h


title: NB2_GW405833_C5D3_rep4_6h


title: NB3_Control_CTR_rep14_6h


title: NB3_Retinoic acid_C11D1_rep4_6h


title: NB3_Control_CTR_rep13_6h


title: NB2_JQ1_C6D1_rep4_6h


title: NB3_Retinoic acid_C11D3_rep4_6h


title: NB3_Rosiglitazone_C12D3_rep4_6h


title: NB2_Control_CTR_rep15_6h


title: NB3_Torin 2_C13D1_rep4_6h


title: NB3_Torin 2_C13D3_rep4_6h


title: NB3_Retinoic acid_C11D2_rep4_6h


title: NB3_Torin 2_C13D2_rep4_6h


title: NB2_JQ1_C6D3_rep4_6h


title: NB2_Lovastatin_C7D3_rep4_6h


title: NB3_DMSO2_DMSO2_rep9_6h


title: NB2_DMSO1_DMSO1_rep7_6h


title: NB2_Fasudil_C4D2_rep4_6h


title: NB2_Fasudil_C4D3_rep4_6h


title: NB2_GW405833_C5D1_rep4_6h


title: NB3_AS601245_C1D1_rep3_6h


title: NB2_Fasudil_C4D1_rep4_6h


title: NB3_Rosiglitazone_C12D1_rep4_6h


title: NB2_DL-PDMP_C3D1_rep4_6h


title: NB2_DL-PDMP_C3D3_rep4_6h


title: NB2_AZDS438_C2D3_rep4_6h


title: NB3_Rosiglitazone_C12D2_rep4_6h


title: NB3_AS601245_C1D2_rep3_6h


title: NB3_AZDS438_C2D2_rep3_6h


title: NB2_Control_CTR_rep13_6h


title: NB2_AZDS438_C2D2_rep4_6h


title: NB2_AZDS438_C2D1_rep4_6h


title: NB3_AS601245_C1D3_rep3_6h


title: NB3_Control_CTR_rep12_6h


title: NB3_AZDS438_C2D3_rep3_6h


title: NB3_DL-PDMP_C3D2_rep3_6h


title: NB3_Fasudil_C4D1_rep3_6h


title: NB3_Fasudil_C4D2_rep3_6h


title: NB3_DL-PDMP_C3D1_rep3_6h


title: NB3_DL-PDMP_C3D3_rep3_6h


title: NB2_DL-PDMP_C3D2_rep4_6h


title: NB2_Torin 2_C13D2_rep3_6h


title: NB2_AS601245_C1D1_rep4_6h


title: NB2_AS601245_C1D3_rep4_6h


title: NB2_AS601245_C1D2_rep4_6h


title: NB2_Torin 2_C13D3_rep3_6h


title: NB2_Torin 2_C13D1_rep3_6h


title: NB2_Rosiglitazone_C12D2_rep3_6h


title: NB2_Rosiglitazone_C12D3_rep3_6h


title: NB3_DMSO1_DMSO1_rep8_6h


title: NB3_AZDS438_C2D1_rep3_6h


title: NB2_Rosiglitazone_C12D1_rep3_6h


title: NB2_Retinoic acid_C11D3_rep3_6h


title: NB2_Control_CTR_rep12_6h


title: NB3_GW405833_C5D2_rep3_6h


title: NB3_JQ1_C6D1_rep3_6h


title: NB3_Control_CTR_rep11_6h


title: NB3_JQ1_C6D3_rep3_6h


title: NB3_JQ1_C6D2_rep3_6h


title: NB3_Lovastatin_C7D3_rep3_6h


title: NB3_Lovastatin_C7D1_rep3_6h


title: NB3_GW405833_C5D3_rep3_6h


title: NB3_Fasudil_C4D3_rep3_6h


title: NB2_DMSO2_DMSO2_rep6_6h


title: NB3_Palbociclib_C9D1_rep4_6h


title: NB3_GW405833_C5D1_rep3_6h


title: NB3_Lovastatin_C7D2_rep3_6h


title: NB2_DMSO1_DMSO1_rep6_6h


title: NB2_PK11195_C10D3_rep3_6h


title: NB3_DMSO2_DMSO2_rep8_6h


title: NB2_Retinoic acid_C11D2_rep3_6h


title: NB2_Retinoic acid_C11D1_rep3_6h


title: NB2_PK11195_C10D2_rep3_6h


title: NB2_PK11195_C10D1_rep3_6h


title: NB2_Palbociclib_C9D3_rep3_6h


title: WT_2_24h

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

institute: University of Geneva Medical School

description:
WT_24h_rep2
WT CD8+ T cells from mice 2 activated for 24h

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads
Genome_build: GRCm38.89
Supplementary_files_format_and_content: Raw counts measurements

source_name: WT CD8+ T cells activated for 24h

growth_protocol: 10 wk old mice were sacrified under isofluoarane anaesthesia, and CD8+ T cells were isolated from spleens using a Miltenyi's magnetic anti-CD8a beads

extract_protocol:
Total RNA was extracted using peqGOLD TriFastTM following the manufacturer’s instructions (PeqLab). Glycogen was used as carrier. RNA purity and integrity were assessed by gel electrophoresis using a Bioanalyzer (Agilent) at the Genomics Platform of the University of Geneva, and RNA was quantified using a Qubit fluorometer.
100 ng cDNA libraries were prepared using the Illumina TruSeq mRNA Stranded Kit according to the manufacturer's protocol.
Libraries were sequenced using single-end reads (50 nt-long) on an Illumina HiSeq4000.

treatment_protocol: CD8+ T cells were cultured in vitro RPMI 1640, GlutaMAXTM medium (Gibco) supplemented with 5% FBS, 50 U/mL penicillin and 50 µg/mL streptomycin and 50 uM b-mercaptoethanol. T cells were activated with plate-coated anti-CD3e (2 ug/ml, clone 145-2C11, BioXCell) and soluble anti-CD28 (2 ug/ml, clone 37.51, Becton Dickinson)

tag: genotype/variation

value: wild type

tag: mouse id #

value: Splenic CD8+ T cells

tag: hrs of activation


title: WT_3_12h

description:
WT_12h_rep3
WT CD8+ T cells from mice 3 activated for 12h

source_name: WT CD8+ T cells activated for 12h

tag: cell type


title: WT_3_24h

description:
WT_24h_rep3
WT CD8+ T cells from mice 3 activated for 24h


title: WT_1_24h

description:
WT_24h_rep1
WT CD8+ T cells from mice 1 activated for 24h


title: WT_2_12h

description:
WT_12h_rep2
WT CD8+ T cells from mice 2 activated for 12h


title: WT_5_24h

description:
WT_24h_rep5
WT CD8+ T cells from mice 5 activated for 24h


title: WT_4_24h

description:
WT_24h_rep4
WT CD8+ T cells from mice 4 activated for 24h


title: WT_3_6h

description:
WT_06h_rep3
WT CD8+ T cells from mice 3 activated for 6h

source_name: WT CD8+ T cells activated for 6h


title: NB2_Palbociclib_C9D1_rep3_6h


title: NB2_Palbociclib_C9D2_rep3_6h


title: NB3_Omiplasib_C8D1_rep3_6h


title: NB3_Control_CTR_rep10_6h


title: WT_2_6h

description:
WT_06h_rep2
WT CD8+ T cells from mice 2 activated for 6h


title: NB3_Omiplasib_C8D3_rep3_6h


title: WT_4_12h

description:
WT_12h_rep4
WT CD8+ T cells from mice 4 activated for 12h


title: NB2_Control_CTR_rep11_6h


title: WT_5_12h

description:
WT_12h_rep5
WT CD8+ T cells from mice 5 activated for 12h


title: WT_1_12h

description:
WT_12h_rep1
WT CD8+ T cells from mice 1 activated for 12h


title: NB3_Omiplasib_C8D2_rep3_6h


title: WT_5_6h

description:
WT_06h_rep5
WT CD8+ T cells from mice 5 activated for 6h


title: NB2_Omiplasib_C8D3_rep3_6h


title: WT_1_6h

description:
WT_06h_rep1
WT CD8+ T cells from mice 1 activated for 6h


title: NB3_Palbociclib_C9D2_rep3_6h


title: WT_4_6h

description:
WT_06h_rep4
WT CD8+ T cells from mice 4 activated for 6h


title: WT_3_2h

description:
WT_02h_rep3
WT CD8+ T cells from mice 3 activated for 2h

source_name: WT CD8+ T cells activated for 2h


title: NB3_PK11195_C10D2_rep3_6h


title: NB2_Omiplasib_C8D2_rep3_6h


title: NB3_Palbociclib_C9D3_rep3_6h


title: WT_2_2h

description:
WT_02h_rep2
WT CD8+ T cells from mice 2 activated for 2h


title: NB3_PK11195_C10D1_rep3_6h


title: WT_1_2h

description:
WT_02h_rep1
WT CD8+ T cells from mice 1 activated for 2h


title: WT_4_2h

description:
WT_02h_rep4
WT CD8+ T cells from mice 4 activated for 2h


title: WT_5_0h

description:
WT_00h_rep5
WT CD8+ T cells from mice 5 activated for 0h

source_name: WT CD8+ T cells activated for 0h

value: 0h - naive


title: WT_3_0h

description:
WT_00h_rep3
WT CD8+ T cells from mice 3 activated for 0h


title: NB3_Retinoic acid_C11D1_rep3_6h

value: Human-derived xenograft neuroblastoma (NB) primary cells


title: NB3_Palbociclib_C9D1_rep3_6h

value: Child


title: NB2_Lovastatin_C7D2_rep3_6h


title: NB2_Lovastatin_C7D3_rep3_6h


title: WT_5_2h

description:
WT_02h_rep5
WT CD8+ T cells from mice 5 activated for 2h


title: NB2_Omiplasib_C8D1_rep3_6h


title: KO_5_24h

description:
KO_24h_rep5
KO CD8+ T cells from mice 5 activated for 24h

source_name: KO CD8+ T cells activated for 24h


title: NB3_DMSO1_DMSO1_rep9_6h


title: NB2_Omiplasib_C8D1_rep4_6h


title: NB2_Lovastatin_C7D1_rep3_6h


title: KO_4_24h

description:
KO_24h_rep4
KO CD8+ T cells from mice 4 activated for 24h


title: KO_3_24h

description:
KO_24h_rep3
KO CD8+ T cells from mice 3 activated for 24h


title: NB2_JQ1_C6D3_rep3_6h


title: NB2_JQ1_C6D1_rep3_6h


title: KO_1_24h

description:
KO_24h_rep1
KO CD8+ T cells from mice 1 activated for 24h


title: NB2_GW405833_C5D3_rep3_6h


title: KO_2_12h

description:
KO_12h_rep2
KO CD8+ T cells from mice 2 activated for 12h

source_name: KO CD8+ T cells activated for 12h


title: KO_3_12h

description:
KO_12h_rep3
KO CD8+ T cells from mice 3 activated for 12h


title: NB3_PK11195_C10D3_rep3_6h


title: WT_2_0h

description:
WT_00h_rep2
WT CD8+ T cells from mice 2 activated for 0h


title: WT_1_0h

description:
WT_00h_rep1
WT CD8+ T cells from mice 1 activated for 0h


title: WT_4_0h

description:
WT_00h_rep4
WT CD8+ T cells from mice 4 activated for 0h


title: NB2_GW405833_C5D1_rep3_6h


title: NB3_Control_CTR_rep9_6h


title: NB2_Control_CTR_rep10_6h


title: NB2_GW405833_C5D2_rep3_6h


title: NB2_DMSO2_DMSO2_rep5_6h


title: NB3_DMSO1_DMSO1_rep7_6h


title: NB3_Retinoic acid_C11D2_rep3_6h


title: KO_4_6h

description:
KO_06h_rep4
KO CD8+ T cells from mice 4 activated for 6h

source_name: KO CD8+ T cells activated for 6h


title: NB3_Rosiglitazone_C12D1_rep3_6h


title: KO_5_6h

description:
KO_06h_rep5
KO CD8+ T cells from mice 5 activated for 6h


title: KO_3_6h

description:
KO_06h_rep3
KO CD8+ T cells from mice 3 activated for 6h


title: KO_1_6h

description:
KO_06h_rep1
KO CD8+ T cells from mice 1 activated for 6h


title: KO_5_12h

description:
KO_12h_rep5
KO CD8+ T cells from mice 5 activated for 12h


title: NB2_JQ1_C6D2_rep3_6h


title: KO_2_24h

description:
KO_24h_rep2
KO CD8+ T cells from mice 2 activated for 24h


title: KO_4_12h

description:
KO_12h_rep4
KO CD8+ T cells from mice 4 activated for 12h


title: KO_2_6h

description:
KO_06h_rep2
KO CD8+ T cells from mice 2 activated for 6h


title: NB3_Rosiglitazone_C12D3_rep3_6h


title: KO_1_12h

description:
KO_12h_rep1
KO CD8+ T cells from mice 1 activated for 12h


title: KO_5_2h

description:
KO_02h_rep5
KO CD8+ T cells from mice 5 activated for 2h

source_name: KO CD8+ T cells activated for 2h


title: NB3_Torin 2_C13D2_rep3_6h


title: NB3_AS601245_C1D1_rep2_6h


title: NB3_Retinoic acid_C11D3_rep3_6h


title: NB3_AS601245_C1D2_rep2_6h


title: KO_1_2h

description:
KO_02h_rep1
KO CD8+ T cells from mice 1 activated for 2h


title: NB3_Torin 2_C13D3_rep3_6h


title: KO_3_0h

description:
KO_00h_rep3
KO CD8+ T cells from mice 3 activated for 0h

source_name: KO CD8+ T cells activated for 0h


title: KO_5_0h

description:
KO_00h_rep5
KO CD8+ T cells from mice 5 activated for 0h


title: KO_3_2h

description:
KO_02h_rep3
KO CD8+ T cells from mice 3 activated for 2h


title: KO_2_2h

description:
KO_02h_rep2
KO CD8+ T cells from mice 2 activated for 2h


title: KO_4_2h

description:
KO_02h_rep4
KO CD8+ T cells from mice 4 activated for 2h


title: KO_4_0h

description:
KO_00h_rep4
KO CD8+ T cells from mice 4 activated for 0h


title: NB3_DMSO2_DMSO2_rep7_6h


title: NB2_Fasudil_C4D2_rep3_6h


title: Acvr1:Nfatc1Cre rep3

city: Ann Arbor

first: Richard

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

data_processing:
Reads were downloaded  and concatenated into a single .fastq.gz file for each sample.  We used FASTQC to assess the quality of reads and trimmed/filtered reads as necessary.
The Tuxedo Suite software package was used for alignment, differential expression analysis, and post-analysis diagnostics [2, 3, 4]. Briefly, we aligned reads to the reference transcriptome mRNAs (UCSC mm10) [5] using TopHat (version 2.0.13) and Bowtie2 (version 2.2.1.).
FastQC was used for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis.
Cufflinks/CuffDiff (version 2.1.1) were used for expression quantitation, normalization, and differential expression analysis, using UCSC mm10.fa as the reference genome sequence.
Genes were declared as differentially expressed if they meet both fold change (+/- 1.5) and FDR (<= 0.05) criteria.
Genome_build: mm10
Supplementary_files_format_and_content: Text file with mapped read counts

source_name: Acvr1:Nfatc1Cre, aortic valve

extract_protocol:
Aortic valves were removed and place in the RLT buffer (Qiagen), and RNA was harvested using the RNEasy kit (Qiagen). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: Outbred

tag: tissue

value: Aortic valve

value: 4-months old

tag: genotype

value: mutant


title: NB2_DL-PDMP_C3D1_rep3_6h

value: DL-PDMP


title: KO_2_0h

description:
KO_00h_rep2
KO CD8+ T cells from mice 2 activated for 0h


title: KO_1_0h

description:
KO_00h_rep1
KO CD8+ T cells from mice 1 activated for 0h


title: NB2_Fasudil_C4D1_rep3_6h

value: Fasudil


title: WT rep3

source_name: WT, aortic valve


title: WT rep2


title: NB3_Torin 2_C13D1_rep3_6h

value: Torin 2


title: NB2_DMSO1_DMSO1_rep5_6h

value: DMSO


title: NB3_Rosiglitazone_C12D2_rep3_6h

value: Rosiglitazone


title: NB2_DL-PDMP_C3D3_rep3_6h


title: Acvr1:Nfatc1Cre rep2


title: NB2_DL-PDMP_C3D2_rep3_6h


title: NB2_AS601245_C1D3_rep3_6h


title: NB2_Control_CTR_rep9_6h

value: Control


title: NB2_AZDS438_C2D1_rep3_6h


title: NB3_Control_CTR_rep8_6h


title: NB2_AZDS438_C2D3_rep3_6h


title: NB2_AZDS438_C2D2_rep3_6h


title: WT rep1


title: Acvr1:Nfatc1Cre rep1